Contacts of the helix formed by residues 27 - 44 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER 5.2 2.5 - - - +
16B MET* 4.4 15.9 - - - -
19B VAL* 4.2 12.3 - - + -
25B GLY 3.6 4.5 - - - +
26B HIS* 1.3 84.7 - - - +
28B GLY* 1.3 61.0 + - - -
30B PRO* 3.3 6.1 - - + +
31B MET* 3.1 43.8 + - + +
260B SER 3.4 18.6 - - - +
261B HIS 3.9 1.6 - - - +
263B ALA 3.2 28.9 - - - +
265B LEU* 3.8 24.0 - - + +
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B HIS 3.4 1.6 - - - -
27B PRO* 1.3 77.9 - - - +
29B ALA* 1.3 58.3 - - - +
32B GLY* 2.8 24.6 + - - -
247B ILE* 3.6 22.8 - - - +
248B GLY* 3.0 18.8 + - - -
260B SER* 2.8 23.1 + - - -
261B HIS* 4.1 1.9 + - - -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B HIS* 5.1 0.4 - - - +
28B GLY* 1.3 69.3 - - - +
30B PRO* 1.4 70.8 - - + +
32B GLY* 3.1 1.1 + - - +
33B MET* 2.8 36.6 + - + +
64B ASN* 4.4 11.7 - - - +
66B HIS* 4.3 13.0 - - + +
67B GLY* 4.4 5.6 - - - +
70B LEU* 5.2 2.2 - - + -
183B ASP* 4.3 13.0 - - - +
247B ILE* 4.1 4.8 - - - +
261B HIS 5.2 1.0 + - - -
672B TPP 3.2 28.1 + - - +
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Residues in contact with PRO 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.1 5.7 - - - +
15B SER* 3.5 30.5 - - - +
26B HIS* 3.3 26.5 - - + +
27B PRO 3.3 5.8 - - - +
29B ALA* 1.4 93.2 - - + +
31B MET* 1.3 60.3 + - - +
33B MET 3.9 0.5 - - - -
34B ALA* 3.1 27.0 + - - +
67B GLY* 3.6 25.4 - - - +
69B MET* 4.5 2.5 - - + -
70B LEU* 3.8 25.2 - - + +
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Residues in contact with MET 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 2.8 61.2 + - + +
15B SER* 5.1 1.8 - - - -
16B MET* 4.3 11.0 - - + -
27B PRO* 3.1 29.3 + - + +
28B GLY 3.6 3.4 - - - +
30B PRO* 1.3 77.5 - - + +
32B GLY* 1.3 58.2 + - - +
33B MET 3.6 0.3 + - - -
248B GLY* 3.6 25.8 - - - +
249B PHE* 3.4 31.3 - - - +
251B SER 4.3 0.9 - - - +
265B LEU* 3.9 27.1 - - + -
273B THR* 3.8 26.7 - - + -
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 4.4 0.2 + - - -
28B GLY 2.8 17.6 + - - -
29B ALA* 3.1 3.8 + - - -
31B MET* 1.3 73.9 - - - +
33B MET* 1.3 62.8 + - - +
34B ALA 3.5 0.4 + - - -
183B ASP* 4.5 1.6 - - - -
218B GLY 4.6 1.7 - - - +
219B HIS* 3.2 22.1 + - - -
245B THR* 3.4 17.5 - - - +
246B ILE 3.4 25.1 - - - -
247B ILE* 4.5 2.0 - - - -
248B GLY 4.1 0.2 - - - +
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Residues in contact with MET 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 2.8 19.6 + - - +
30B PRO 3.9 0.7 - - - -
32B GLY* 1.3 71.2 - - - +
34B ALA* 1.3 63.9 + - - +
35B ASP 3.3 2.9 - - - -
36B ILE* 3.1 29.3 + - + +
37B ALA* 2.9 23.3 + - - +
64B ASN* 3.5 27.4 - - - -
70B LEU* 3.9 17.5 - - + -
152B PHE* 3.6 43.1 - - + -
181B PHE* 4.4 9.9 - - + +
183B ASP* 3.3 39.5 - - + +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.5 27.0 - - - +
11B ILE* 3.9 18.3 - - + +
12B ARG* 3.7 24.2 - - + +
30B PRO 3.1 16.9 + - - +
31B MET 3.8 0.4 + - - -
32B GLY 3.5 2.6 - - - -
33B MET* 1.3 76.9 - - - +
35B ASP* 1.3 57.0 + - - +
37B ALA* 3.3 3.9 + - - +
38B GLU* 2.9 29.5 + - - +
70B LEU* 4.5 0.4 - - - -
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Residues in contact with ASP 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 4.6 13.0 - - - +
8B ALA* 3.1 15.5 - - - +
12B ARG* 2.8 36.9 + - - +
32B GLY 5.0 0.2 + - - -
33B MET 3.3 0.6 - - - -
34B ALA* 1.3 73.2 - - - +
36B ILE* 1.3 65.5 + - - +
38B GLU* 3.3 3.8 + - - +
39B VAL* 3.2 27.0 + - - +
218B GLY 3.5 12.5 + - - +
219B HIS* 2.8 34.2 + - - +
221B ALA* 5.4 3.9 - - + +
224B ILE* 3.8 8.7 - - + -
249B PHE* 4.9 2.6 - - - -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B MET* 3.1 27.9 + - + +
35B ASP* 1.3 75.6 - - - +
37B ALA* 1.3 58.8 + - - +
39B VAL* 3.3 3.6 + - - +
40B LEU* 3.0 27.0 + - - +
152B PHE* 3.8 15.3 - - + -
181B PHE* 3.5 35.4 - - + -
218B GLY* 3.6 14.8 - - - +
224B ILE* 3.8 20.7 - - + +
243B CYS* 3.6 30.3 - - + -
245B THR* 3.7 22.2 - - + -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.2 1.3 - - + -
33B MET 2.9 16.3 + - - +
34B ALA 3.7 4.5 - - - +
36B ILE* 1.3 77.4 - - - +
38B GLU* 1.3 57.2 + - - +
40B LEU* 4.5 1.3 - - - +
41B TRP* 2.9 37.2 + - - +
70B LEU* 3.8 23.8 - - + -
74B LEU* 4.0 19.7 - - + -
152B PHE* 4.0 20.2 - - + -
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 2.8 56.1 + - - +
7B LEU* 4.0 5.7 - - + +
8B ALA* 4.0 12.6 - - + +
34B ALA 2.9 17.0 + - - +
35B ASP* 3.6 5.4 - - - +
36B ILE 3.3 0.4 - - - -
37B ALA* 1.3 75.9 - - - +
39B VAL* 1.3 63.3 + - - +
42B ARG* 2.7 71.4 + - - +
221B ALA* 4.7 1.2 - - - +
294B TRP* 3.7 30.7 - - + -
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 3.6 12.1 - - - +
35B ASP 3.2 13.4 + - - +
36B ILE 3.9 5.6 - - - +
38B GLU* 1.3 79.8 - - - +
40B LEU* 1.3 67.2 + - - +
43B ASP* 3.0 26.2 + - + +
44B PHE* 3.6 14.6 - - + -
221B ALA* 3.8 39.0 - - + +
224B ILE* 3.9 13.2 - - + +
225B LYS* 3.7 31.4 - - + +
228B VAL* 4.9 1.6 - - + -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE 3.0 17.4 + - - +
37B ALA* 4.0 2.7 - - - +
39B VAL* 1.3 77.6 - - - +
41B TRP* 1.3 68.4 + - + +
44B PHE* 3.1 20.8 + - + -
45B LEU* 2.9 30.3 + - + +
60B PHE* 3.9 22.0 - - + -
150B TYR* 3.7 46.4 - - + -
152B PHE* 3.8 26.0 - - + -
181B PHE* 3.9 22.0 - - + -
224B ILE* 5.4 0.2 - - - +
228B VAL* 5.1 2.5 - - + -
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Residues in contact with TRP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 2.9 23.3 + - + +
40B LEU* 1.3 96.5 - - + +
42B ARG* 1.3 60.3 + - - +
45B LEU* 3.6 42.4 + - + +
47B HIS* 3.9 27.3 + + - -
60B PHE* 3.7 46.5 - + + -
71B ILE* 4.8 4.0 - - + -
74B LEU* 3.7 46.8 - - + +
75B LEU* 4.0 20.2 - - + -
78B THR* 3.9 27.9 - - + +
80B TYR* 4.2 8.5 - + - -
108B GLY 5.7 1.8 - - - -
294B TRP* 4.2 7.4 - - + -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.9 2.4 - - - +
7B LEU* 3.5 14.6 - - - +
38B GLU* 2.7 55.4 + - - +
41B TRP* 1.3 77.9 - - - +
43B ASP* 1.3 66.7 + - - +
78B THR* 5.9 0.4 - - + -
293B GLN* 2.8 43.6 + - - +
294B TRP* 3.7 39.7 - - + +
678B EDO 2.8 41.0 + - - -
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 2.9 43.1 + - - -
39B VAL* 3.0 15.1 + - + +
42B ARG* 1.3 88.8 + - - +
44B PHE* 1.3 78.4 + - + +
225B LYS* 2.9 29.4 + - - +
678B EDO 4.9 4.9 + - - -
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.6 26.2 - - + -
40B LEU* 3.1 16.7 + - + +
42B ARG 3.8 0.6 - - - -
43B ASP* 1.3 99.4 - - + +
45B LEU* 1.3 69.3 + - - +
46B LYS* 3.2 5.9 + - - +
58B ASP* 3.8 4.7 - - - +
150B TYR* 4.0 15.4 + - - +
225B LYS* 4.0 14.8 - - + -
228B VAL* 3.8 22.9 - - + -
229B GLU* 3.8 30.1 - - + -
232B ARG* 3.5 42.2 + - - +
303B LYS* 5.3 2.7 + - - -
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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