Contacts of the helix formed by residues 35 - 57 (chain B) in PDB entry 4GUN
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 LYS 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASN* 3.5 45.7 - - + +
183A VAL* 6.1 1.3 - - - +
30B ASP 5.0 0.7 - - - +
31B LEU* 2.9 29.8 + - + +
34B ASN* 1.4 86.4 - - + +
36B HIS* 1.4 59.1 + - - +
37B HIS 3.6 0.4 - - - -
38B VAL* 3.5 3.5 + - - +
39B ALA* 3.0 29.9 + - - +
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Residues in contact with HIS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 3.9 6.0 + - - -
177A TYR* 2.7 38.1 + + - -
182A ASN* 3.8 20.5 - - + +
31B LEU* 2.9 33.7 + - + -
32B HIS* 3.4 22.2 - - + +
35B LYS* 1.4 69.7 - - - +
37B HIS* 1.3 61.2 + - - +
39B ALA* 3.3 18.2 + - - +
40B TYR* 3.2 25.0 + - + -
174B HIS* 3.5 42.7 + + + +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.5 8.6 - - + +
11B PRO* 3.4 19.5 - - + +
32B HIS 3.0 15.5 + - - +
33B ILE* 3.4 14.8 + - - +
36B HIS* 1.3 68.5 - - - +
38B VAL* 1.3 66.7 + - - +
40B TYR* 3.0 19.9 + - + -
41B VAL* 3.0 18.5 + - + +
77B HIS* 2.9 41.5 + - - -
80B HIS* 3.5 19.5 - - + +
81B SER* 3.3 21.7 + - - -
84B TRP* 2.9 27.3 + - + -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.9 23.6 - - + -
33B ILE 3.4 13.3 + - - +
34B ASN* 3.3 32.5 - - - +
35B LYS 3.5 4.0 + - - +
36B HIS 3.3 0.4 - - - -
37B HIS* 1.3 75.8 - - - +
39B ALA* 1.4 55.5 + - - +
41B VAL* 3.3 7.7 + - + +
42B ASN* 3.0 47.6 + - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS 3.0 14.5 + - - +
36B HIS* 3.3 13.4 + - - +
38B VAL* 1.4 75.4 - - - +
40B TYR* 1.3 60.9 + - + +
42B ASN* 4.1 5.7 - - - +
43B GLY* 3.0 26.0 + - - -
73B HIS* 3.6 9.5 + - + -
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.7 1.1 - - - -
36B HIS* 3.2 29.9 + - + -
37B HIS* 3.0 13.1 + - - +
39B ALA* 1.3 75.3 - - + +
41B VAL* 1.3 67.2 + - - +
44B TYR* 2.9 27.8 + - - +
72B PHE* 3.6 26.9 - + - -
73B HIS* 3.5 36.0 - + - +
76B GLY* 3.7 11.2 - - - -
77B HIS* 3.8 10.8 - - - +
80B HIS* 3.3 34.3 - + - -
155B GLN* 2.8 26.6 + - + -
172B TRP* 3.9 16.3 - - - -
174B HIS* 4.2 6.6 - - - -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.6 32.4 - - + +
9B SER* 3.9 7.4 - - - -
10B LEU* 3.8 25.8 - - + +
37B HIS* 3.0 32.5 + - + +
38B VAL* 3.5 10.1 - - + +
40B TYR* 1.3 75.5 - - - +
42B ASN* 1.4 67.8 + - - +
44B TYR* 3.8 2.1 - - - +
45B ASN* 3.2 33.5 + - - +
77B HIS* 3.9 13.0 - - - +
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Residues in contact with ASN 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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38B VAL* 3.0 36.8 + - - +
39B ALA* 4.1 5.6 - - - +
41B VAL* 1.4 78.7 - - - +
43B GLY* 1.3 59.8 + - - +
45B ASN* 3.5 7.9 + - - +
46B ALA* 3.0 29.9 + - - +
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA 3.0 18.7 + - - -
42B ASN* 1.3 73.2 - - - +
44B TYR* 1.4 58.4 + - - +
46B ALA* 3.4 6.8 + - - +
47B ALA* 2.9 29.8 + - - +
73B HIS* 3.6 26.0 - - - -
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Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 4.0 14.2 + - - -
8B ILE* 3.7 35.9 - - + -
40B TYR 2.9 17.2 + - - +
43B GLY* 1.4 73.8 - - - +
45B ASN* 1.4 70.6 + - - +
47B ALA* 3.2 5.4 + - - +
48B ILE* 2.9 64.1 + - + +
70B ILE* 4.1 9.4 - - + -
73B HIS* 3.3 14.1 - - + +
74B GLY* 3.6 22.0 - - - -
55D VAL* 4.3 7.1 + - - +
60D LEU* 3.3 28.1 - - + +
63D VAL* 3.7 25.1 - - + +
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Residues in contact with ASN 45 (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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2B ILE* 3.4 21.1 - - + +
7B LYS* 3.3 22.6 - - + +
8B ILE* 2.9 48.4 + - - +
41B VAL* 3.2 22.9 + - - +
42B ASN* 3.9 7.2 + - - +
43B GLY 3.4 0.2 - - - -
44B TYR* 1.4 80.1 - - - +
46B ALA* 1.4 61.3 + - - +
49B ASP* 3.2 21.1 + - - +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASN 3.0 18.0 + - - +
43B GLY* 3.6 7.9 - - - +
45B ASN* 1.4 76.2 - - - +
47B ALA* 1.4 57.0 + - - +
49B ASP* 3.4 7.1 + - - +
50B ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY 2.9 17.9 + - - +
44B TYR 3.2 4.2 + - - +
46B ALA* 1.4 73.1 - - - +
48B ILE* 1.3 55.4 + - - +
50B ALA* 3.3 2.8 + - - +
51B LEU* 2.7 38.0 + - - +
66B ILE* 3.4 11.6 - - + +
69B ASN* 4.1 16.8 - - + +
70B ILE* 3.8 32.8 - - + +
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Residues in contact with ILE 48 (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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2B ILE* 3.6 26.7 - - + -
6B GLU* 4.0 2.5 - - + +
44B TYR* 2.9 59.6 + - + +
47B ALA* 1.3 73.9 - - - +
49B ASP* 1.3 57.5 + - - +
51B LEU* 3.5 5.4 - - + +
52B GLU* 3.1 58.4 + - + +
70B ILE* 4.1 21.5 - - + -
51D LEU* 5.4 2.9 - - + -
55D VAL* 3.7 29.8 - - + -
63D VAL* 4.6 0.2 - - + -
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Residues in contact with ASP 49 (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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2B ILE* 3.0 43.6 + - + +
45B ASN 3.2 14.4 + - - +
46B ALA* 3.5 10.3 - - - +
48B ILE* 1.3 75.2 - - - +
50B ALA* 1.4 63.2 + - - +
52B GLU* 3.6 2.8 + - - +
53B LYS* 3.4 53.8 + - - +
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Residues in contact with ALA 50 (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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46B ALA 2.9 17.5 + - - +
47B ALA* 3.8 5.4 - - - +
49B ASP* 1.4 74.9 - - - +
51B LEU* 1.4 61.5 + - - +
53B LYS* 3.5 13.1 + - - +
54B ALA* 3.1 18.4 + - - +
66B ILE* 3.4 27.7 - - + +
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Residues in contact with LEU 51 (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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47B ALA 2.7 21.3 + - - +
48B ILE* 3.5 9.9 - - + +
49B ASP 3.3 0.2 - - - -
50B ALA* 1.4 72.2 - - - +
52B GLU* 1.3 61.3 + - + +
54B ALA* 3.2 1.6 + - - -
55B VAL* 2.8 61.2 + - + +
63B VAL* 4.3 11.9 - - + +
66B ILE* 3.9 8.0 - - + +
67B GLN* 3.1 30.5 - - - +
70B ILE* 3.7 20.6 - - + -
48D ILE* 5.3 0.9 - - + -
51D LEU* 3.5 31.6 - - + -
55D VAL* 5.9 0.2 - - + -
70D ILE* 5.7 0.2 - - + -
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Residues in contact with GLU 52 (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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2B ILE* 3.4 22.1 + - - +
3B THR* 5.8 0.7 - - - +
6B GLU* 2.8 38.1 - - - +
48B ILE* 3.1 26.9 + - + +
49B ASP 4.1 3.8 - - - +
51B LEU* 1.3 81.3 - - + +
53B LYS* 1.3 56.4 + - - +
55B VAL* 3.9 6.1 - - - +
56B GLY* 3.0 26.5 + - - -
6D GLU* 5.0 1.9 - - - +
51D LEU* 6.4 0.7 - - + -
52D GLU* 6.2 3.7 - - + +
55D VAL* 3.6 7.4 - - - +
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Residues in contact with LYS 53 (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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49B ASP* 3.4 45.6 + - - +
50B ALA* 3.7 12.3 - - - +
51B LEU 3.3 0.2 - - - -
52B GLU* 1.3 75.8 - - + +
54B ALA* 1.4 61.6 + - - +
56B GLY* 3.4 3.3 + - - -
57B LYS* 3.3 33.3 + - + +
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Residues in contact with ALA 54 (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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50B ALA 3.1 17.0 + - - +
51B LEU 3.7 2.0 - - - +
53B LYS* 1.4 72.1 - - - +
55B VAL* 1.4 64.0 + - - +
57B LYS* 3.2 17.9 + - - +
58B ARG 3.2 3.8 + - - -
59B ASP* 3.0 27.4 + - - +
62B SER* 3.9 15.7 - - - -
63B VAL* 3.6 19.5 - - + -
66B ILE* 3.7 16.6 - - + -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 2.8 42.6 + - + +
52B GLU* 4.0 5.2 - - - +
54B ALA* 1.4 70.4 - - - +
56B GLY* 1.3 62.4 + - - +
58B ARG* 3.3 12.2 + - - +
63B VAL* 3.6 18.8 - - + -
6D GLU* 3.4 41.0 - - + +
44D TYR* 4.0 6.2 + - - +
48D ILE* 3.7 42.8 - - + -
52D GLU* 4.3 3.8 - - + +
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Residues in contact with GLY 56 (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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52B GLU 3.0 18.1 + - - -
53B LYS* 3.7 2.9 - - - -
54B ALA 3.3 0.2 - - - -
55B VAL* 1.3 77.3 - - - +
57B LYS* 1.3 57.1 + - - +
58B ARG 3.8 0.2 + - - -
5D ASN* 2.7 34.8 + - - +
6D GLU* 3.9 15.0 - - - -
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Residues in contact with LYS 57 (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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53B LYS* 3.3 16.6 + - + +
54B ALA* 3.2 26.5 + - - +
56B GLY* 1.3 76.0 - - - +
58B ARG* 1.4 68.2 + - - +
59B ASP* 3.2 31.0 + - + +
62B SER* 4.8 1.8 + - - -
5D ASN 5.3 0.2 - - - -
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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