Contacts of the helix formed by residues 27 - 44 (chain A) in PDB entry 2R5N
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 PRO 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A SER 5.3 2.2 - - - +
16A MET* 4.5 14.8 - - - -
19A VAL* 4.2 11.9 - - + -
25A GLY 3.5 5.2 - - - +
26A HIS* 1.3 85.9 - - - +
28A GLY* 1.3 67.5 + - - +
29A ALA 3.5 0.2 - - - -
30A PRO* 3.3 6.1 - - + +
31A MET* 3.1 44.7 + - + +
260A SER 3.5 11.9 - - - +
261A HIS 4.0 1.8 - - - +
263A ALA 3.2 28.9 - - - +
265A LEU* 3.9 24.7 - - + +
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Residues in contact with GLY 28 (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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26A HIS 3.4 1.4 - - - -
27A PRO* 1.3 77.6 - - - +
29A ALA* 1.3 57.4 + - - +
32A GLY* 2.9 25.3 + - - -
247A ILE* 3.6 23.1 - - - +
248A GLY* 3.0 18.3 + - - -
260A SER* 2.8 23.1 + - - -
261A HIS* 4.0 2.1 + - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS 5.0 0.4 - - - -
28A GLY* 1.3 71.7 - - - +
30A PRO* 1.4 74.1 - - + +
32A GLY* 3.2 0.8 + - - +
33A MET* 2.9 29.8 + - + +
64A ASN* 4.5 10.5 - - - +
66A HIS* 4.1 14.3 - - + +
67A GLY* 4.4 6.3 - - - -
70A LEU* 5.2 1.6 - - + -
183A ASP* 4.4 12.3 - - - +
247A ILE* 4.2 4.3 - - - +
261A HIS 5.1 1.4 + - - -
672A TPP 3.2 29.2 + - - +
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Residues in contact with PRO 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 4.2 3.2 - - + +
12A ARG* 5.6 0.2 - - - -
15A SER* 3.5 31.9 - - - +
26A HIS 3.2 26.7 - - - +
27A PRO 3.3 5.8 - - - +
29A ALA* 1.4 92.7 - - + +
31A MET* 1.3 60.6 + - - +
33A MET 3.9 0.3 - - - -
34A ALA* 3.1 27.0 + - - +
67A GLY* 3.7 25.6 - - - +
69A MET* 4.5 2.7 - - + -
70A LEU* 3.8 26.7 - - + +
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Residues in contact with MET 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.8 61.2 + - + +
15A SER* 5.2 2.0 - - - -
16A MET* 4.1 11.7 - - + -
27A PRO* 3.1 28.2 + - + +
28A GLY 3.7 2.9 - - - +
30A PRO* 1.3 78.6 - - + +
32A GLY* 1.3 58.6 + - - +
33A MET 3.5 0.2 + - - -
248A GLY* 3.7 20.9 - - - +
249A PHE* 3.5 26.9 - - - +
251A SER* 4.3 1.3 - - - +
265A LEU* 3.8 27.8 - - + -
273A THR* 3.7 27.6 - - + -
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Residues in contact with GLY 32 (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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12A ARG* 4.4 0.2 + - - -
28A GLY 2.9 14.5 + - - -
29A ALA* 3.2 4.4 + - - -
31A MET* 1.3 78.4 - - - +
33A MET* 1.3 60.7 + - - +
34A ALA 3.5 0.4 + - - -
183A ASP* 5.1 1.1 - - - -
218A GLY 4.7 1.9 - - - +
219A HIS* 3.2 21.7 + - - -
245A THR* 3.3 17.5 - - - +
246A ILE 3.4 25.1 - - - -
247A ILE* 4.5 2.0 - - - -
248A GLY 4.0 0.4 - - - +
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Residues in contact with MET 33 (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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29A ALA* 2.9 17.5 + - - +
30A PRO 3.9 0.7 - - - -
32A GLY* 1.3 76.0 - - - +
34A ALA* 1.3 59.7 + - - +
35A ASP 3.3 2.9 - - - -
36A ILE* 3.1 31.0 + - + +
37A ALA* 2.9 28.0 + - - +
64A ASN* 3.5 27.4 - - - -
70A LEU* 3.9 17.0 - - + -
152A PHE* 3.5 43.1 - - + -
153A MET 5.1 0.2 - - - +
181A PHE* 4.5 9.9 - - + +
182A TYR 5.2 0.2 - - - -
183A ASP* 3.3 38.6 - - + +
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Residues in contact with ALA 34 (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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8A ALA* 3.5 26.7 - - - +
11A ILE* 3.8 16.4 - - + +
12A ARG* 3.6 25.4 - - + +
30A PRO 3.1 17.2 + - - +
31A MET 3.8 0.2 + - - -
32A GLY 3.5 2.0 - - - -
33A MET* 1.3 77.1 - - - +
35A ASP* 1.3 56.9 + - - +
37A ALA* 3.4 3.5 + - - +
38A GLU* 2.9 29.6 + - - +
70A LEU* 4.5 1.3 - - - -
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Residues in contact with ASP 35 (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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4A ARG 5.5 0.2 - - - -
5A LYS* 4.5 13.9 - - - +
8A ALA* 3.2 15.3 - - - +
12A ARG* 2.7 38.9 + - - +
32A GLY 5.0 0.2 + - - -
33A MET 3.3 0.6 - - - -
34A ALA* 1.3 72.6 - - - +
36A ILE* 1.3 65.8 + - - +
38A GLU* 3.4 3.8 + - - +
39A VAL* 3.2 28.2 + - - +
218A GLY 3.5 13.0 + - - +
219A HIS* 2.8 34.9 + - - +
221A ALA* 5.3 5.1 - - + +
224A ILE* 3.9 7.0 - - + -
249A PHE* 4.8 2.6 - - - -
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Residues in contact with ILE 36 (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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33A MET* 3.1 28.0 + - + +
35A ASP* 1.3 77.8 - - - +
37A ALA* 1.3 62.1 + - - +
39A VAL* 3.3 4.0 + - - +
40A LEU* 3.0 21.8 + - - +
152A PHE* 3.7 16.6 - - + -
181A PHE* 3.4 35.4 - - + -
183A ASP* 4.7 0.2 - - - +
218A GLY* 3.7 13.5 - - - +
224A ILE* 3.9 20.7 - - + +
243A CYS* 3.6 28.7 - - + -
245A THR* 3.7 22.2 - - + -
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Residues in contact with ALA 37 (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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11A ILE* 4.1 1.1 - - + -
33A MET 2.9 15.0 + - - +
34A ALA 3.7 4.5 - - - +
36A ILE* 1.3 77.7 - - - +
38A GLU* 1.3 56.5 + - - +
40A LEU* 4.6 0.2 - - - -
41A TRP* 2.8 38.5 + - - +
70A LEU* 3.8 24.2 - - + -
74A LEU* 3.9 23.6 - - + -
152A PHE* 4.0 17.0 - - + -
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Residues in contact with GLU 38 (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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4A ARG* 2.8 56.3 + - - +
7A LEU* 4.0 4.3 - - + +
8A ALA* 4.0 13.5 - - + +
34A ALA 2.9 16.9 + - - +
35A ASP* 3.7 5.0 - - - +
36A ILE 3.3 0.4 - - - -
37A ALA* 1.3 76.9 - - - +
39A VAL* 1.3 61.9 + - - +
42A ARG* 2.8 72.4 + - - +
221A ALA* 4.6 1.0 - - - +
294A TRP* 3.8 29.1 - - + -
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Residues in contact with VAL 39 (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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4A ARG* 3.7 11.7 - - - +
35A ASP 3.2 13.4 + - - +
36A ILE 3.3 5.6 + - - +
38A GLU* 1.3 79.8 - - - +
40A LEU* 1.3 67.4 + - - +
43A ASP* 2.9 31.2 + - + +
44A PHE* 3.7 15.1 - - + -
221A ALA* 3.6 39.9 - - + +
224A ILE* 3.9 13.7 - - + +
225A LYS* 3.8 31.6 - - + +
228A VAL* 4.9 1.3 - - + -
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Residues in contact with LEU 40 (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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36A ILE 3.0 17.0 + - - +
37A ALA* 4.0 3.6 - - - +
39A VAL* 1.3 76.6 - - - +
41A TRP* 1.3 66.8 + - + +
44A PHE* 3.1 21.3 + - + -
45A LEU* 2.9 29.3 + - + +
60A PHE* 3.9 23.8 - - + -
150A TYR* 3.6 46.7 - - + -
152A PHE* 3.8 26.0 - - + -
181A PHE* 3.9 23.3 - - + -
224A ILE* 5.4 0.4 - - - +
228A VAL* 5.2 2.5 - - + -
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Residues in contact with TRP 41 (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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37A ALA* 2.8 23.4 + - - +
40A LEU* 1.3 95.6 - - + +
42A ARG* 1.3 60.6 + - - +
43A ASP 3.7 0.2 + - - -
44A PHE 4.4 0.2 + - - -
45A LEU* 3.5 42.9 + - + +
47A HIS* 3.9 24.0 + + - -
60A PHE* 3.7 44.1 - + + -
71A ILE* 4.8 4.3 - - + -
74A LEU* 3.7 44.1 - - + +
75A LEU* 3.8 22.2 - - + -
78A THR* 3.9 35.0 - - + +
80A TYR* 4.2 9.0 - + - -
108A GLY 5.6 1.8 - - - -
294A TRP* 4.3 7.6 - - + -
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Residues in contact with ARG 42 (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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4A ARG* 4.0 11.5 - - - +
7A LEU* 3.3 21.1 - - - +
38A GLU* 2.8 57.8 + - - +
41A TRP* 1.3 77.7 - - - +
43A ASP* 1.3 69.1 + - - +
78A THR* 5.8 0.4 - - + -
293A GLN* 2.9 38.7 + - - +
294A TRP* 3.6 39.9 - - + +
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Residues in contact with ASP 43 (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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4A ARG* 2.9 42.3 + - - -
39A VAL* 2.9 16.0 + - + +
42A ARG* 1.3 87.8 + - - +
44A PHE* 1.3 78.9 + - + +
225A LYS* 2.9 30.0 + - - +
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Residues in contact with PHE 44 (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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39A VAL* 3.7 25.8 - - + -
40A LEU* 3.1 16.7 + - + +
42A ARG 3.8 0.4 - - - -
43A ASP* 1.3 97.2 - - + +
45A LEU* 1.3 69.9 + - - +
46A LYS* 3.2 5.7 + - - +
58A ASP* 3.9 4.4 - - - +
150A TYR* 4.0 15.3 + - - +
225A LYS* 3.9 16.8 - - + -
228A VAL* 3.7 24.0 - - + -
229A GLU* 3.7 30.5 - - + -
232A ARG* 3.6 41.9 + - - -
303A LYS* 5.2 3.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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