Contacts of the helix formed by residues 298 - 319 (chain A) in PDB entry 2WWR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 3.9 16.1 + - + -
296A SER 3.2 3.4 + - - -
297A ALA* 1.3 80.9 - - - +
299A HIS* 1.3 56.2 + - - +
300A ARG* 3.9 7.6 + - - +
301A THR* 2.8 28.9 + - - -
302A ARG* 2.8 33.1 + - - +
124B ARG* 4.0 12.1 - - - +
147B CYS* 3.9 8.7 - - - -
148B GLY 3.4 25.8 - - - +
150B GLY* 4.1 15.9 - - - +
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 1.3 72.0 - - - +
300A ARG* 1.3 63.5 + - - +
302A ARG* 4.6 2.7 - - - -
303A ASN* 2.9 60.6 + - - +
144B LEU* 3.6 28.5 - - + +
147B CYS* 3.9 14.4 - - + +
148B GLY 4.4 3.2 + - - +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 4.0 7.8 - - - +
299A HIS* 1.3 83.5 + - - +
301A THR* 1.3 64.4 + - - +
303A ASN* 3.7 4.3 - - - +
304A THR* 3.2 26.7 + - - +
152B THR 4.1 10.7 + - - -
153B GLN* 2.6 45.8 + - - +
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.9 11.0 + - - +
107A LEU* 3.8 28.7 - - + -
110A THR* 2.5 31.9 + - - +
296A SER* 3.6 18.2 - - - +
298A THR* 2.8 18.5 + - - -
300A ARG* 1.3 78.5 - - - +
302A ARG* 1.3 58.0 + - - +
304A THR* 3.3 6.6 + - - -
305A MET* 2.9 31.4 + - - +
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 3.7 12.0 - - + +
81A MET* 4.0 5.1 - - - +
293A HIS 4.2 6.9 + - - -
294A ILE* 4.6 0.4 - - - +
296A SER* 2.8 42.4 + - - +
297A ALA* 3.4 27.9 - - - +
298A THR 2.8 25.1 + - - +
299A HIS* 4.1 3.8 - - - +
301A THR* 1.3 72.9 - - - +
303A ASN* 1.3 57.5 + - - +
305A MET* 3.4 14.9 + - - +
306A SER* 3.0 29.1 + - - -
141B TRP* 3.4 33.1 - - - +
142B LYS 3.2 18.0 + - - -
143B PRO* 2.8 45.4 + - - +
144B LEU* 4.9 3.1 - - + -
145B TRP 4.7 3.8 + - - +
147B CYS* 4.3 3.8 - - - -
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Residues in contact with ASN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 3.1 24.2 - - - +
17A ALA* 4.0 4.5 + - - +
18A GLU* 3.7 40.9 + - + +
299A HIS* 2.9 52.6 + - - +
300A ARG* 3.7 4.2 - - - +
302A ARG* 1.3 77.4 - - - +
304A THR* 1.3 57.1 + - - +
306A SER* 3.2 4.0 - - - -
307A LEU* 2.9 27.0 + - - +
144B LEU* 5.5 0.2 - - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 4.5 7.3 + - - -
106A VAL* 3.5 33.0 - - + +
300A ARG* 3.2 20.3 + - - +
301A THR* 3.7 6.1 - - - -
303A ASN* 1.3 74.8 - - - +
305A MET* 1.3 65.8 + - - +
307A LEU* 3.4 8.9 + - + +
308A LEU* 3.0 24.0 + - + +
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Residues in contact with MET 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 3.5 36.1 - - + +
82A SER* 4.4 2.5 - - - -
103A THR* 3.6 17.0 - - - +
106A VAL* 3.8 19.0 - - + +
107A LEU* 3.6 28.5 - - + -
296A SER* 3.6 26.9 - - - +
301A THR* 2.9 21.3 + - + +
302A ARG* 3.6 18.4 - - - +
304A THR* 1.3 74.5 - - - +
306A SER* 1.3 57.1 + - - +
308A LEU 3.2 1.6 + - - -
309A ALA* 2.9 31.5 + - - +
141B TRP* 4.2 16.8 - - + -
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Residues in contact with SER 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.6 10.4 - - - +
16A PRO* 3.1 45.6 + - - +
19A GLY* 3.3 12.7 - - - -
81A MET* 4.1 12.0 - - - +
302A ARG 3.0 14.2 + - - -
303A ASN 3.2 9.9 - - - -
305A MET* 1.3 77.4 - - - +
307A LEU* 1.3 61.1 + - - +
309A ALA* 3.5 2.8 + - - +
310A ALA* 3.2 22.7 + - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.7 31.6 - - + +
19A GLY* 4.2 6.0 - - - -
22A ALA* 4.1 19.5 - - + -
303A ASN 2.9 16.9 + - - +
304A THR* 3.8 8.7 - - + +
305A MET 3.3 0.2 - - - -
306A SER* 1.3 74.8 - - - +
308A LEU* 1.3 58.4 + - - +
310A ALA* 3.2 4.2 + - - +
311A ASN* 2.9 56.4 + - - +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR 3.8 4.9 - - - +
103A THR* 3.7 32.5 - - + -
104A PRO 4.4 9.0 - - - +
106A VAL* 4.8 15.3 - - + -
304A THR* 3.0 18.1 + - + +
305A MET* 3.7 3.6 - - - +
307A LEU* 1.3 74.2 - - - +
309A ALA* 1.3 59.5 + - - +
311A ASN* 3.2 7.5 + - + +
312A ASN* 2.8 42.6 + - - +
323A PRO* 3.6 33.4 - - + +
324A SER* 3.9 15.5 - - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 6.2 0.2 - - + -
56A LEU* 4.1 16.6 - - + +
79A SER* 2.6 32.4 + - - +
81A MET* 4.0 32.5 - - + +
103A THR* 4.0 6.2 - - + +
305A MET 2.9 19.0 + - - +
306A SER* 3.7 4.7 - - - +
308A LEU* 1.3 72.7 - - - +
310A ALA* 1.3 62.7 + - - +
312A ASN* 4.4 1.3 - - - +
313A LEU* 3.1 11.4 + - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY* 4.0 11.9 - - - +
22A ALA* 3.9 25.4 - - + -
23A LEU* 4.0 14.1 - - + +
56A LEU* 4.0 12.1 - - + +
306A SER 3.2 14.1 + - - +
307A LEU 3.5 8.1 - - - +
309A ALA* 1.3 74.5 - - - +
311A ASN* 1.3 60.1 + - - +
313A LEU* 3.1 3.2 + - - +
314A LEU* 2.9 34.8 + - + +
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Residues in contact with ASN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 4.7 6.1 - - - +
307A LEU* 2.9 49.7 + - - +
308A LEU* 3.8 7.4 - - - +
310A ALA* 1.3 74.7 - - - +
312A ASN* 1.3 64.7 + - - +
314A LEU* 3.3 9.8 + - - +
315A ALA* 2.9 27.0 + - - +
323A PRO* 4.0 21.0 - - + +
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Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.2 1.1 - - - +
79A SER* 3.4 16.1 + - - +
101A GLY* 4.0 0.9 - - - -
102A TYR 3.0 34.8 + - - +
308A LEU* 2.8 32.7 + - - +
309A ALA* 4.5 1.2 - - - +
311A ASN* 1.3 72.2 - - - +
313A LEU* 1.3 55.6 + - - +
315A ALA 3.5 0.2 + - - -
316A GLY* 3.0 25.3 + - - -
322A MET* 3.6 26.8 - - + +
323A PRO* 3.2 15.2 - - - +
324A SER* 3.1 34.9 + - - +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.7 37.2 - - + -
23A LEU* 3.8 19.3 - - + -
54A GLY 4.0 0.4 - - - -
55A LEU 3.4 43.5 - - - +
56A LEU* 3.8 10.5 - - + +
77A VAL* 3.6 18.1 - - + +
79A SER* 3.8 13.4 + - - +
309A ALA 3.1 13.8 + - - +
310A ALA* 3.1 8.7 + - - +
312A ASN* 1.3 75.2 - - - +
314A LEU* 1.3 63.2 + - - +
316A GLY* 3.2 2.3 + - - -
317A LEU* 3.0 33.1 + - + +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.8 0.2 - - + -
22A ALA* 3.6 31.0 - - + +
23A LEU* 4.0 17.5 - - + -
26A ALA* 3.9 23.8 - - + -
29A CYS* 3.9 19.1 - - - -
310A ALA 2.9 21.0 + - - +
311A ASN* 3.9 10.5 - - - +
313A LEU* 1.3 77.2 - - - +
315A ALA* 1.3 61.5 + - - +
317A LEU* 3.6 9.3 + - + +
318A ARG* 3.3 54.1 + - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASN 2.9 17.2 + - - +
312A ASN 3.9 3.1 - - - +
314A LEU* 1.3 73.5 - - - +
316A GLY* 1.3 64.2 + - - +
318A ARG 3.3 1.0 + - - -
319A GLY 3.0 4.3 + - - -
320A GLU* 2.9 49.5 + - + +
321A PRO 3.9 21.1 - - - +
322A MET* 4.0 12.3 - - + -
323A PRO* 4.4 3.1 - - + -
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 4.2 11.4 - - - +
77A VAL* 4.1 20.2 - - - -
99A ARG* 4.0 23.2 + - - -
312A ASN 3.0 15.8 + - - -
313A LEU 3.2 3.6 + - - -
315A ALA* 1.3 76.8 - - - +
317A LEU* 1.3 60.2 + - - +
319A GLY* 3.3 12.5 + - - -
322A MET* 4.1 3.0 - - - +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET* 3.7 28.7 - - + +
9A VAL* 3.8 25.8 - - + -
29A CYS* 4.0 17.9 - - - -
53A HIS* 3.6 44.4 - - + +
54A GLY 3.8 2.7 - - - +
76A LYS* 2.8 30.4 + - - +
77A VAL* 3.8 8.3 - - + +
313A LEU* 3.0 29.0 + - + +
314A LEU* 3.8 11.2 - - + +
316A GLY* 1.3 76.1 - - - +
318A ARG* 1.3 59.9 + - + +
319A GLY 3.3 0.2 - - - -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 5.0 4.2 - - + +
26A ALA* 3.9 26.7 - - - +
27A ALA 5.0 1.0 - - - +
28A ASP* 3.0 33.5 + - - +
76A LYS* 5.3 0.7 - - - -
314A LEU* 3.3 44.0 + - - +
315A ALA 3.3 1.8 + - - +
316A GLY 3.2 0.8 - - - -
317A LEU* 1.3 77.0 - - + +
319A GLY* 1.3 62.4 + - - +
320A GLU* 3.5 35.0 + - + +
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 5.0 2.6 - - - +
99A ARG* 3.7 15.8 + - - -
315A ALA 3.0 3.4 + - - -
316A GLY 3.3 6.4 + - - -
317A LEU 3.3 1.0 + - - -
318A ARG* 1.3 80.1 - - - +
320A GLU* 1.3 61.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il