Contacts of the helix formed by residues 292 - 309 (chain A) in PDB entry 1EFA
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 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 3.3 14.0 - - + -
290A LYS* 3.9 26.0 + - + +
291A GLN* 1.3 66.4 - - - +
293A PHE* 1.3 64.4 + - - +
294A ARG* 3.0 23.2 + - - +
295A LEU* 3.0 38.0 + - + +
296A LEU 3.2 8.7 + - - -
320A PRO 5.4 1.9 + - - +
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Residues in contact with PHE 293 (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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74A HIS* 4.1 20.2 - + - -
75A ALA* 3.6 19.5 - - + -
78A GLN* 3.8 32.8 - - + -
79A ILE* 4.1 19.2 - - + +
82A ALA* 3.8 6.0 - - - +
161A PHE* 4.3 2.2 - + - -
274A ASP* 3.7 32.8 - - + -
276A THR* 5.4 1.8 - - + -
291A GLN* 2.9 32.0 + - + -
292A ASP* 1.3 68.7 + - - +
294A ARG* 1.3 66.4 + - - +
296A LEU* 3.2 7.7 + - - +
297A GLY* 3.0 19.4 + - - -
901A NPF 3.4 33.9 - - + -
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLN 5.5 0.6 + - - -
81A ALA* 3.5 7.5 + - - +
82A ALA* 3.2 47.0 + - - +
85A SER* 3.3 28.7 + - - -
292A ASP* 3.0 11.0 + - - +
293A PHE* 1.3 77.2 - - - +
295A LEU* 1.3 53.5 + - - +
297A GLY 3.2 0.2 + - - -
298A GLN* 2.8 37.8 + - - +
70B SER* 5.6 1.8 + - - -
72B ALA* 5.9 2.0 - - - +
98B MET* 5.0 0.4 - - - +
100B GLU* 3.6 10.3 + - - -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 5.2 2.7 - - + -
292A ASP* 3.0 32.6 + - + +
294A ARG* 1.3 80.1 - - - +
296A LEU* 1.3 56.0 + - - +
298A GLN* 3.7 16.6 - - - +
299A THR* 2.7 50.7 + - - +
319A LEU* 4.4 19.7 - - + -
320A PRO* 4.6 19.5 - - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.5 33.9 - - + -
148A LEU* 4.1 20.4 - - + +
159A ILE* 3.8 21.5 - - + +
160A ILE* 4.9 2.5 - - - +
161A PHE* 3.8 31.0 - - + -
292A ASP 3.2 3.8 + - - -
293A PHE 3.2 6.9 + - - +
295A LEU* 1.3 80.6 - - - +
297A GLY* 1.3 54.5 + - - +
299A THR* 3.7 0.9 - - - -
300A SER* 2.6 46.2 + - - +
319A LEU* 3.5 24.4 - - + +
901A NPF 4.0 10.5 - - + +
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Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 4.2 5.5 - - - +
82A ALA* 3.8 19.7 - - - -
83A ILE* 3.9 18.5 - - - +
293A PHE 3.0 11.1 + - - -
294A ARG 3.7 2.2 - - - -
296A LEU* 1.3 74.0 - - - +
298A GLN* 1.3 65.3 + - - +
300A SER* 3.4 3.6 + - - -
301A VAL* 3.3 28.4 + - - +
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Residues in contact with GLN 298 (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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82A ALA 4.3 2.1 + - - +
86A ARG* 3.4 41.8 - - + +
294A ARG 2.8 21.7 + - - +
295A LEU* 3.7 24.8 - - - +
297A GLY* 1.3 73.6 - - - +
299A THR* 1.3 70.1 + - - +
301A VAL 3.4 0.5 + - - -
302A ASP* 2.6 52.1 + - - +
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Residues in contact with THR 299 (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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159A ILE* 3.7 20.6 - - + -
295A LEU* 2.7 38.6 + - - +
296A LEU* 3.7 5.2 - - - -
298A GLN* 1.3 85.6 + - - +
300A SER* 1.3 58.7 + - - +
302A ASP* 3.3 3.5 + - + +
303A ARG* 2.8 31.2 + - + +
317A GLN* 4.0 23.1 - - - +
319A LEU* 4.6 6.9 - - + +
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 4.8 2.5 - - - -
123A ILE* 3.9 19.2 - - - +
146A LEU* 3.5 18.2 - - - +
148A LEU* 3.6 30.8 - - - +
159A ILE* 4.0 2.7 - - - +
296A LEU* 2.6 32.5 + - - +
297A GLY* 3.6 8.6 - - - -
298A GLN 3.3 0.2 - - - -
299A THR* 1.3 73.2 - - - +
301A VAL* 1.3 57.9 + - - +
303A ARG 3.5 0.2 + - - -
304A LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.7 24.5 - - + -
83A ILE* 3.6 41.5 - - + +
86A ARG* 3.5 22.9 - - + -
87A ALA* 4.2 8.7 - - + +
90A LEU* 3.9 15.9 - - + -
92A ALA* 5.3 0.4 - - + -
123A ILE* 4.5 5.4 - - + -
297A GLY 3.3 13.2 + - - +
298A GLN 3.8 0.2 - - - +
299A THR 3.2 0.2 - - - -
300A SER* 1.3 73.9 - - - +
302A ASP* 1.3 69.0 + - - +
304A LEU* 3.1 4.0 + - - +
305A LEU* 3.0 26.1 + - + +
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Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 3.2 37.8 + - - -
90A LEU* 3.6 5.2 - - - +
298A GLN* 2.6 34.8 + - - +
299A THR* 3.7 7.6 - - + +
301A VAL* 1.3 75.4 - - - +
303A ARG* 1.3 59.0 + - - +
305A LEU* 3.2 8.7 + - - +
306A GLN* 3.0 41.1 + - - +
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.5 33.6 - - + +
157A ASN* 4.2 5.9 - - - +
158A SER 3.1 13.6 + - - +
159A ILE* 3.4 9.4 - - + +
299A THR* 2.8 20.3 + - + +
302A ASP* 1.3 74.3 - - - +
304A LEU* 1.3 66.5 + - - +
306A GLN* 3.2 23.9 + - - +
307A LEU* 3.0 26.9 + - + +
313A VAL* 3.2 32.5 + - - +
315A GLY 3.6 18.2 + - - -
316A ASN 4.2 1.0 - - - -
317A GLN* 2.8 52.7 + - - +
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Residues in contact with LEU 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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64A ILE* 3.5 42.0 - - + -
120A SER* 6.1 0.2 - - - +
121A GLY* 3.6 24.2 - - - -
122A LEU 3.4 26.7 - - - +
123A ILE* 3.9 11.4 - - + -
144A PRO* 3.8 18.8 - - + +
145A ALA 4.7 0.2 - - - -
146A LEU* 4.3 11.4 - - + +
300A SER 2.9 21.2 + - - +
301A VAL* 3.1 4.5 + - - +
303A ARG* 1.3 74.3 - - - +
305A LEU* 1.3 58.9 + - + +
307A LEU* 3.6 6.9 + - + +
308A SER* 3.0 25.3 + - - -
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Residues in contact with LEU 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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62A LEU* 3.8 41.1 - - + -
64A ILE* 4.2 19.1 - - + -
90A LEU* 3.4 35.4 - - + -
92A ALA* 4.9 2.2 - - + -
120A SER* 5.6 2.2 - - - +
301A VAL* 3.0 22.4 + - + +
302A ASP* 3.5 7.9 - - - +
304A LEU* 1.3 75.5 - - + +
306A GLN* 1.3 66.1 + - + +
308A SER* 3.0 12.3 + - - -
309A GLN* 3.0 34.1 + - - +
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Residues in contact with GLN 306 (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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302A ASP* 3.0 29.9 + - - +
303A ARG* 3.5 19.1 - - - +
305A LEU* 1.3 75.3 - - - +
307A LEU* 1.3 57.9 + - - +
309A GLN* 2.8 22.0 + - - -
311A GLN* 3.0 57.0 + - + +
313A VAL* 3.6 28.9 - - + +
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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
----------------------------------------------------------
144A PRO* 4.0 20.9 - - + +
145A ALA 4.4 7.0 - - - +
146A LEU* 4.6 3.6 - - + -
157A ASN* 3.8 27.4 - - + +
303A ARG* 3.0 31.4 + - + +
304A LEU* 3.6 13.7 - - + +
306A GLN* 1.3 77.1 - - - +
308A SER* 1.3 58.9 + - - +
310A GLY* 2.8 22.4 + - - +
311A GLN 4.3 7.6 - - - +
313A VAL* 3.7 29.2 - - + +
314A LYS* 4.0 31.0 + - + +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 3.3 32.9 + - - -
144A PRO* 3.9 11.7 - - - +
304A LEU 3.0 15.1 + - - -
305A LEU* 3.0 19.6 + - - -
307A LEU* 1.3 76.6 - - - +
309A GLN* 1.3 56.7 + - - +
310A GLY 3.2 2.9 + - - -
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Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.0 20.0 + - - +
306A GLN* 2.8 12.7 + - - +
308A SER* 1.3 79.0 - - - +
310A GLY* 1.3 60.5 + - - +
311A GLN* 2.8 19.4 + - + +
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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