Contacts of the helix formed by residues 298 - 312 (chain A) in PDB entry 5W97
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 ASP 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A GLY 5.0 1.2 - - - +
297A MET* 1.3 78.9 - - - +
299A VAL* 1.3 64.5 + - - +
300A ASP* 4.2 9.0 - - + +
301A THR* 3.2 17.2 + - - +
302A ARG* 2.9 21.9 + - - +
304C PGV 3.6 38.4 + - - +
22H ASN* 3.3 40.7 - - - +
23H GLN 5.7 0.2 - - - +
24H ASN* 5.7 0.2 - - - +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ASP* 1.3 72.2 - - - +
300A ASP* 1.3 66.3 + - - +
302A ARG* 3.2 17.4 + - - +
303A ALA* 2.9 27.9 + - - +
84B LEU* 3.8 34.5 - - + +
85B TYR* 3.7 35.7 - - + -
88B ASP* 3.6 34.0 + - + +
22H ASN* 4.5 10.9 - - - +
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ASP* 3.2 6.3 - - + +
299A VAL* 1.3 82.6 - - - +
301A THR* 1.3 63.3 + - - +
303A ALA* 3.1 4.4 + - - +
304A TYR* 3.0 18.0 + - - +
85B TYR* 2.7 35.4 + - - -
301C CHD 3.7 25.9 + - + +
22H ASN* 5.9 0.9 + - - -
103g CDL 3.4 29.6 + - - +
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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
----------------------------------------------------------
297A MET* 4.2 22.0 - - + -
298A ASP* 3.2 25.2 + - - +
300A ASP* 1.3 78.3 - - - +
302A ARG* 1.3 63.4 + - - +
304A TYR* 3.0 15.4 + - - +
305A PHE* 3.1 36.2 + - + -
301C CHD 2.6 43.2 + - + +
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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
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293A PHE* 3.7 48.9 + - + +
297A MET* 2.9 43.9 + - + +
298A ASP 2.9 9.1 + - - +
299A VAL* 3.3 29.6 - - - +
301A THR* 1.3 75.8 - - - +
303A ALA* 1.3 57.7 + - - +
305A PHE* 4.7 0.7 - - - -
306A THR* 3.2 32.2 + - - -
361A SER* 3.4 10.1 + - - +
365A ILE* 5.2 3.0 - - - +
84B LEU* 3.5 32.5 + - + +
87B MET* 4.5 11.3 - - - +
88B ASP* 3.7 16.4 + - - +
23H GLN* 3.6 22.8 + - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL 2.9 13.1 + - - +
300A ASP 3.4 8.5 - - - +
301A THR 3.1 0.4 - - - -
302A ARG* 1.3 74.3 - - - +
304A TYR* 1.3 67.2 + - - +
306A THR* 3.6 2.3 + - - -
307A SER* 3.0 27.1 + - - -
81B LEU* 3.9 24.8 - - + +
84B LEU* 4.0 2.5 - - + -
85B TYR* 3.5 24.0 - - + +
103g CDL 4.4 14.1 - - + +
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Residues in contact with TYR 304 (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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286A ILE* 2.9 51.5 + - - +
288A TRP* 6.2 0.2 - + - -
300A ASP 3.0 5.6 + - - +
301A THR 3.0 7.5 + - - +
303A ALA* 1.3 77.0 - - - +
305A PHE* 1.3 87.7 + + - +
307A SER* 2.8 7.0 + - - -
308A ALA* 2.8 42.1 + - + +
301C CHD 3.5 37.0 - - + -
103g CDL 3.7 70.1 + - + +
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Residues in contact with PHE 305 (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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286A ILE 3.4 24.7 - - - -
287A VAL* 3.7 21.5 - - - -
288A TRP* 3.8 27.6 - + - -
289A ALA* 3.3 36.6 - - + -
290A HIS 4.5 2.0 - - - +
293A PHE* 4.0 21.8 - - + -
297A MET* 5.1 0.4 - - + -
301A THR* 3.1 40.1 + - + +
302A ARG* 4.7 0.7 - - - -
304A TYR* 1.3 93.8 - + - +
306A THR* 1.3 63.1 + - - +
308A ALA* 4.4 1.5 - - - +
309A THR* 2.6 34.0 + - - -
301C CHD 4.1 15.9 - - + -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.3 4.6 - - - -
302A ARG 3.2 12.8 + - - -
303A ALA 3.9 4.3 - - - -
305A PHE* 1.3 76.6 - - - +
307A SER* 1.3 65.8 + - - +
309A THR* 3.9 2.2 - - - -
310A MET* 3.3 32.1 + - + +
359A ALA 2.8 27.8 + - - +
360A ASN* 4.0 18.4 - - - +
361A SER* 2.8 25.2 + - - +
77B ALA* 6.0 0.9 - - + -
80B SER* 4.5 4.5 - - - +
81B LEU* 4.4 17.0 - - + -
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 3.0 14.6 + - - -
304A TYR 2.8 10.4 + - - -
306A THR* 1.3 79.6 - - - +
308A ALA* 1.3 60.6 + - - -
310A MET* 3.3 15.3 + - - +
311A ILE* 3.6 18.5 + - - +
77B ALA* 5.3 0.7 - - - +
81B LEU* 3.9 8.0 - - - +
103g CDL 3.6 62.7 - - - +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.7 4.3 - - + +
286A ILE* 4.2 6.1 - - + +
287A VAL* 3.8 19.5 - - + +
304A TYR* 2.8 49.8 + - + +
305A PHE* 4.4 2.2 - - - +
307A SER* 1.3 70.8 - - - +
309A THR* 1.3 65.3 + - - +
310A MET 3.3 0.5 + - - -
311A ILE* 3.3 25.1 + - - +
312A ILE* 4.0 3.6 + - - +
103g CDL 4.5 10.0 - - + +
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Residues in contact with THR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 6.0 0.4 - - - +
287A VAL* 3.6 15.9 + - + +
290A HIS* 2.7 38.1 + - + +
305A PHE 2.6 22.8 + - - -
306A THR* 3.9 4.3 - - - -
307A SER 3.3 0.2 - - - -
308A ALA* 1.3 77.1 - - - +
310A MET* 1.3 61.5 + - - +
312A ILE* 3.3 22.3 + - + +
313A ALA 4.5 0.3 + - - -
356A ILE* 4.6 0.2 - - - +
359A ALA* 3.6 17.0 - - + -
602A HEA 3.6 31.2 - - + +
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Residues in contact with MET 310 (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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306A THR* 3.3 22.2 + - + +
307A SER* 3.8 7.4 - - - +
308A ALA 3.2 1.0 - - - -
309A THR* 1.3 75.3 - - - +
311A ILE* 1.3 65.0 + - - +
312A ILE 3.1 2.7 + - - -
313A ALA* 3.2 13.5 + - - +
356A ILE* 4.3 19.5 - - + +
359A ALA* 4.1 15.0 - - + -
360A ASN* 4.4 8.5 - - - +
73B LEU* 3.2 47.2 - - + +
76B ILE* 4.3 19.5 - - - -
77B ALA* 3.4 36.6 - - + -
103g CDL 4.5 10.1 - - + -
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.8 24.2 - - + -
307A SER 3.6 15.0 - - - +
308A ALA* 3.3 15.4 + - - +
310A MET* 1.3 76.1 - - - +
312A ILE* 1.3 63.3 + - - +
314A ILE* 3.0 23.4 + - + +
315A PRO* 3.2 6.9 - - - +
73B LEU* 4.7 3.8 - - + -
303c PEK 4.1 27.1 - - + -
30g LEU* 4.7 16.4 - - + -
103g CDL 3.5 52.0 - - + -
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Residues in contact with ILE 312 (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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244A TYR* 4.0 20.0 - - + +
280A ILE* 4.2 15.7 - - + +
283A LEU* 3.4 48.5 - - + +
284A GLY* 3.9 7.6 - - - +
287A VAL* 4.6 6.5 - - + -
308A ALA 4.3 3.6 - - - +
309A THR* 3.4 22.9 - - + +
310A MET 3.1 0.8 - - - -
311A ILE* 1.3 76.7 - - - +
313A ALA* 1.3 60.2 + - - +
314A ILE 3.2 0.7 + - - -
315A PRO* 3.3 4.9 - - - +
316A THR* 2.7 34.4 + - - +
602A HEA 3.4 29.6 - - + +
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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
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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