Contacts of the helix formed by residues 58 - 78 (chain B) in PDB entry 3D9M
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 TYR 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.1 36.3 + - + -
15B ASN* 3.5 33.0 + - - -
17B TYR 2.5 24.9 + - - -
18B LYS* 4.6 0.3 - - - -
19B PRO* 3.7 23.7 - - + +
21B ILE* 4.5 2.5 - - + -
50B PHE* 3.8 16.0 - + + -
54B CYS* 3.7 14.9 - - + -
55B LYS* 2.9 30.5 + - + +
57B GLU* 1.3 96.3 - - + +
59B LYS* 1.3 58.3 + - - +
60B VAL 3.4 1.8 - - - -
61B PRO* 3.5 12.0 - - + +
62B GLY* 2.9 27.4 + - - -
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 2.6 32.3 + - + +
52B GLN* 3.6 12.1 + - - +
54B CYS* 3.1 32.0 + - - -
55B LYS 4.2 1.8 - - - -
56B PRO* 3.1 23.6 + - + +
58B TYR* 1.3 76.1 - - - +
60B VAL* 1.3 60.6 + - + +
62B GLY* 3.0 4.1 + - - -
63B LEU 3.0 23.0 + - - -
98B ASN* 3.6 22.0 + - - +
99B LEU* 3.2 38.5 - - + +
101B ARG* 4.4 12.6 - - - +
102B CYS* 3.9 14.4 - - + -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO 4.7 1.0 + - - -
57B GLU 4.7 0.8 + - - -
59B LYS* 1.3 76.1 - - - +
61B PRO* 1.3 65.0 - - + +
63B LEU* 3.0 8.8 + - + +
64B TYR* 2.8 64.2 + - + +
99B LEU* 5.2 0.2 - - - -
102B CYS* 4.9 2.0 - - + -
106B ASP* 3.7 46.4 - - + +
109B LYS* 4.1 17.0 - - + +
110B ILE* 4.1 16.8 - - + -
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Residues in contact with PRO 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.4 12.8 - - + -
19B PRO* 4.1 13.2 - - + -
20B PRO* 5.9 0.2 - - + -
21B ILE* 3.8 32.8 - - + +
26B MET* 4.0 2.5 - - + +
57B GLU 3.3 24.0 - - - +
58B TYR* 3.5 14.8 - - + +
60B VAL* 1.3 96.0 - - + +
62B GLY* 1.3 55.3 + - - +
64B TYR* 3.2 14.6 + - + +
65B VAL* 2.9 32.8 + - - +
106B ASP* 5.6 0.2 - - - +
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Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.9 0.4 - - - -
47B VAL* 4.3 1.6 - - - +
50B PHE* 4.3 12.7 - - - -
51B ILE* 3.8 24.1 - - - +
58B TYR 2.9 18.7 + - - -
59B LYS 3.0 5.1 + - - -
61B PRO* 1.3 72.0 - - - +
63B LEU* 1.3 61.8 + - - +
65B VAL* 3.2 18.0 + - - +
66B ILE* 3.2 16.1 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LYS 3.0 11.3 + - - +
60B VAL* 3.0 11.2 + - + +
62B GLY* 1.3 75.8 - - - +
64B TYR* 1.3 61.3 + - + +
66B ILE* 3.1 11.0 + - + +
67B ASP* 2.9 25.3 + - - +
96B PHE* 3.8 15.7 - - + -
99B LEU* 3.9 18.2 - - + +
109B LYS 4.7 0.7 - - - +
110B ILE* 3.8 45.1 - - + +
113B VAL* 3.8 24.9 - - + -
117B TRP* 3.7 31.0 - - + -
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Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO* 6.4 2.0 - - + -
21B ILE* 6.1 4.9 - - + -
26B MET* 3.8 10.1 - - + -
60B VAL* 2.8 43.4 + - + +
61B PRO* 3.4 14.8 - - + +
63B LEU* 1.3 75.0 - - + +
65B VAL* 1.3 53.2 + - - +
67B ASP* 3.5 5.5 - - + +
68B SER* 2.8 36.6 + - - -
109B LYS* 4.1 18.8 + - - +
112B ARG* 5.6 3.6 + - - -
113B VAL* 3.6 31.2 - - + -
1Z TYR* 3.7 46.2 - + + -
3Z PRO* 4.0 20.2 - - + +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.1 11.9 - - + -
14B LEU* 4.1 20.9 - - + -
26B MET* 3.7 21.3 - - - -
29B ILE* 3.9 20.2 - - + -
47B VAL* 3.9 19.5 - - + -
61B PRO 2.9 18.9 + - - +
62B GLY* 3.2 10.7 + - - +
64B TYR* 1.3 73.4 - - - +
66B ILE* 1.3 65.9 + - - +
68B SER* 3.4 1.3 + - - -
69B ILE* 3.0 45.8 + - + +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.7 19.7 - - + -
48B GLU* 5.9 0.4 - - + -
51B ILE* 3.8 21.5 - - + -
62B GLY 3.2 4.7 + - - +
63B LEU* 3.1 18.4 + - + +
65B VAL* 1.3 75.8 - - - +
67B ASP* 1.3 64.0 + - - +
69B ILE* 3.9 0.5 - - - +
70B VAL* 2.9 29.9 + - + +
88B PHE* 3.7 44.4 - - + -
92B ILE* 6.3 1.8 - - + -
95B THR* 3.9 17.7 - - + -
96B PHE* 5.5 2.7 - - + -
117B TRP* 3.9 23.3 - - + -
123B PHE* 4.4 4.3 - - + -
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU 2.9 12.8 + - - +
64B TYR* 3.5 12.3 - - + +
66B ILE* 1.3 78.1 - - - +
68B SER* 1.3 56.4 + - - +
70B VAL* 4.0 1.7 - - - +
71B ARG* 2.9 62.6 + - - +
113B VAL* 4.3 6.8 - - + +
116B LEU* 5.9 1.2 - - - +
117B TRP* 2.8 38.8 + - + +
1Z TYR* 2.6 23.5 + - + +
3Z PRO* 3.5 21.8 - - + +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MET* 3.8 11.1 + - - +
27B THR* 5.4 0.7 - - - -
30B THR* 2.6 28.1 + - - +
64B TYR 2.8 21.7 + - - -
65B VAL 3.9 2.5 - - - -
67B ASP* 1.3 73.4 - - - +
69B ILE* 1.3 57.8 + - - +
71B ARG* 4.0 2.6 - - - +
72B GLN* 2.9 33.1 + - - +
1Z TYR* 3.3 29.4 + - - -
7Z SER* 5.2 0.2 + - - -
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 4.2 5.8 - - + -
29B ILE* 5.0 0.2 - - + -
30B THR* 4.0 17.7 - - - +
33B ALA* 3.7 27.6 - - + -
34B ILE* 4.4 2.9 - - + +
43B VAL* 4.3 4.0 - - + -
47B VAL* 4.2 14.4 - - + -
65B VAL* 3.0 42.3 + - + +
66B ILE 3.9 2.7 - - - +
68B SER* 1.3 75.5 - - - +
70B VAL* 1.3 58.8 + - - +
72B GLN* 3.3 1.4 + - - +
73B SER* 2.8 29.5 + - - -
84B PHE* 3.5 44.6 - - + -
88B PHE* 4.4 9.2 - - + -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 2.9 22.2 + - + +
67B ASP* 4.0 3.1 - - - +
69B ILE* 1.3 76.2 - - - +
71B ARG* 1.3 58.0 + - - +
73B SER* 3.8 1.3 - - - -
74B ARG* 3.0 39.0 + - - +
82B ASP* 4.2 1.7 - - - +
84B PHE* 4.1 7.4 - - + -
85B ALA* 3.8 28.5 - - + +
88B PHE* 3.7 27.4 - - + -
122B VAL* 3.4 32.1 - - + -
123B PHE* 4.1 11.2 - - + -
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 2.9 42.8 + - - +
68B SER* 4.2 2.4 - - - +
70B VAL* 1.3 76.8 - - - +
72B GLN* 1.3 62.4 + - - +
74B ARG* 3.5 8.2 + - - +
75B HIS* 3.1 19.4 + - - +
117B TRP* 5.4 0.4 - - - -
122B VAL* 4.6 26.7 - - + -
506B SO4 2.9 47.7 + - - +
1Z TYR* 2.9 28.9 + - - -
2Z SER 3.8 2.8 + - - -
3Z PRO 3.5 19.1 + - - -
4Z THR 4.9 0.8 - - - -
5Z SEP 2.8 31.5 + - - -
6Z PRO 5.0 1.2 + - - -
7Z SER* 3.4 13.2 + - - +
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Residues in contact with GLN 72 (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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30B THR* 3.5 24.2 - - + -
31B LYS* 6.3 0.2 - - - -
34B ILE* 4.0 15.0 - - + -
68B SER* 2.9 20.5 + - - +
69B ILE 3.9 0.9 - - - +
71B ARG* 1.3 77.0 - - - +
73B SER* 1.3 56.9 + - - +
75B HIS* 3.3 10.8 + - - +
76B GLN* 2.9 55.0 + - - +
7Z SER* 3.4 33.7 + - - +
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Residues in contact with SER 73 (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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34B ILE* 3.9 12.3 - - - +
69B ILE 2.8 18.3 + - - -
70B VAL 3.8 1.3 - - - -
72B GLN* 1.3 74.8 - - - +
74B ARG* 1.3 59.0 + - - +
77B PHE* 2.8 37.0 + - - +
78B GLY 4.2 0.7 - - - +
82B ASP* 2.7 28.0 + - - -
84B PHE* 3.6 14.4 - - - -
401B NH4 2.7 25.5 + - - -
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Residues in contact with ARG 74 (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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70B VAL* 3.0 40.1 + - - +
71B ARG* 3.8 8.3 - - - +
73B SER* 1.3 74.3 - - - +
75B HIS* 1.3 58.2 + - - +
78B GLY* 2.9 36.1 + - - -
79B GLN* 3.3 64.2 + - + +
80B GLU* 5.6 1.0 + - - -
82B ASP* 3.7 21.9 + - + +
85B ALA* 5.6 1.0 - - - +
120B ASN 3.9 11.3 + - - -
121B ASN* 3.5 26.0 + - - +
122B VAL* 3.8 23.9 + - - +
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ARG 3.1 13.9 + - - +
72B GLN* 3.5 19.1 - - - +
73B SER 3.2 0.2 - - - -
74B ARG* 1.3 79.7 - - - +
76B GLN* 1.3 63.9 + - - +
78B GLY* 4.2 2.4 + - - -
506B SO4 4.9 9.8 + - - +
7Z SER* 4.1 32.0 + - - +
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Residues in contact with GLN 76 (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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34B ILE* 3.5 32.0 - - - +
72B GLN* 2.9 40.0 + - - +
75B HIS* 1.3 82.2 - - + +
77B PHE* 1.3 81.2 + - + +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.8 35.0 - - + -
37B ILE* 3.6 35.0 - - + -
73B SER* 2.8 22.7 + - - +
76B GLN* 1.3 92.6 - - + +
78B GLY* 1.3 62.3 + - - +
81B LYS* 3.4 25.9 - - + +
401B NH4 3.6 22.4 - - - +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG 2.9 16.9 + - - +
75B HIS 4.2 1.9 + - - -
76B GLN 3.7 0.8 - - - -
77B PHE* 1.3 78.9 - - - +
79B GLN* 1.3 66.9 + - - -
80B GLU 3.2 2.9 - - - -
81B LYS* 3.2 3.3 + - - -
82B ASP* 3.1 24.6 + - - +
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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
------------------------------------------------------------
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