Contacts of the helix formed by residues 57 - 80 (chain B) in PDB entry 1C04
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 GLU 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER* 3.3 18.8 + - - +
56B ASP* 1.3 85.4 - - - +
58B LYS* 1.3 66.1 + - - +
59B HIS* 3.5 33.1 + - + +
60B HIS* 3.6 4.2 + - - +
61B ARG* 3.2 18.6 + - - -
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Residues in contact with LYS 58 (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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57B GLU* 1.3 70.4 - - - +
59B HIS* 1.3 69.7 + - - +
60B HIS 3.1 2.0 - - - -
61B ARG* 2.9 25.1 + - + +
62B ALA* 2.9 15.4 + - + +
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Residues in contact with HIS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 5.6 0.7 - - - -
57B GLU* 3.5 38.6 + - + +
58B LYS* 1.3 79.6 + - - +
60B HIS* 1.3 97.4 + + - +
62B ALA* 3.5 7.4 + - - +
63B LEU* 2.9 38.4 + - + +
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 3.3 19.3 + - - -
40B MET* 3.8 11.4 - - + +
53B ARG* 4.0 7.2 - - + -
54B PRO* 3.2 36.6 - - + +
55B SER* 2.6 44.3 + - - +
57B GLU* 3.6 7.0 + - - +
58B LYS 3.1 0.8 - - - -
59B HIS* 1.3 108.6 + + - +
61B ARG* 1.3 60.8 + - - +
63B LEU* 3.1 8.3 + - + +
64B HIS* 2.8 31.5 + - - +
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 3.8 29.0 + - - +
56B ASP* 2.8 57.2 + - - +
57B GLU 3.2 10.1 + - - +
58B LYS* 2.9 13.6 + - + +
60B HIS* 1.3 78.2 - - - +
62B ALA* 1.3 60.7 + - - +
64B HIS* 3.4 3.3 - - - +
65B GLY* 3.3 18.0 + - - -
68B ARG* 5.6 0.2 + - - -
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Residues in contact with ALA 62 (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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58B LYS* 2.9 20.3 + - + +
59B HIS* 3.7 8.3 - - - +
61B ARG* 1.3 75.6 - - - +
63B LEU* 1.3 63.9 + - - +
65B GLY* 3.6 1.5 + - - +
66B THR* 2.9 29.7 + - - +
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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
----------------------------------------------------------
37B HIS* 3.8 57.0 - - + +
39B ASP* 5.3 0.2 - - - +
40B MET* 3.6 19.3 - - + -
59B HIS* 2.9 27.5 + - + +
60B HIS* 3.1 14.3 + - + +
62B ALA* 1.3 76.6 - - - +
64B HIS* 1.3 50.1 + - - +
66B THR* 3.3 9.7 + - + -
67B THR* 2.8 45.1 + - - +
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.8 6.9 - - - -
51B VAL* 2.7 47.9 + - + +
53B ARG* 2.8 47.7 + - + +
60B HIS 2.8 16.4 + - - +
61B ARG 3.4 7.0 - - - +
63B LEU* 1.3 76.2 - - - +
65B GLY* 1.3 58.3 + - - +
67B THR* 3.5 2.4 + - - -
68B ARG* 3.1 53.4 + - - +
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Residues in contact with GLY 65 (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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61B ARG 3.3 10.6 + - - -
62B ALA* 4.2 1.6 - - - -
63B LEU 3.4 0.2 - - - -
64B HIS* 1.3 76.4 - - - +
66B THR* 1.3 55.4 + - - +
68B ARG* 3.5 24.2 + - - +
69B SER* 2.8 37.1 + - - -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 2.9 23.2 + - - +
63B LEU* 3.3 10.5 + - + -
65B GLY* 1.3 73.9 - - - +
67B THR* 1.3 64.6 + - - +
69B SER* 3.4 5.5 + - - -
70B LEU* 3.2 45.1 + - + +
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Residues in contact with THR 67 (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 PHE* 3.8 29.9 - - + +
37B HIS* 5.2 2.1 + - - +
40B MET* 3.4 19.8 - - + +
42B ILE* 4.2 15.3 - - + -
51B VAL* 3.8 26.7 - - + -
63B LEU* 2.8 29.3 + - - +
64B HIS 3.7 4.3 - - - -
66B THR* 1.3 69.8 - - - +
68B ARG* 1.3 66.3 + - - +
70B LEU* 3.4 5.3 + - - +
71B LEU* 3.1 24.8 + - + +
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Residues in contact with ARG 68 (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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7B PRO* 5.6 9.4 - - + -
8B ILE* 3.8 25.7 - - + +
51B VAL* 4.1 15.2 - - + +
53B ARG* 5.2 0.6 - - - +
64B HIS* 3.1 60.1 + - - +
65B GLY* 3.5 21.7 - - - +
67B THR* 1.3 76.7 - - - +
69B SER* 1.3 63.5 + - - +
71B LEU* 3.3 4.2 + - - +
72B ALA* 2.9 22.2 + - - +
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY 2.8 19.6 + - - -
66B THR* 3.7 6.9 - - - -
67B THR 3.3 0.2 - - - -
68B ARG* 1.3 76.8 - - - +
70B LEU* 1.3 67.7 + - - +
72B ALA* 3.0 9.7 + - - +
73B ASN* 2.9 32.4 + - - -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 3.5 42.8 - - - +
36B PHE* 3.6 24.2 - - + -
66B THR* 3.2 30.6 + - + +
67B THR* 3.6 3.8 - - - +
68B ARG 3.4 0.2 - - - -
69B SER* 1.3 82.7 - - - +
71B LEU* 1.3 62.1 + - - +
73B ASN* 3.5 9.8 + - - +
74B MET* 3.0 27.6 + - - +
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Residues in contact with LEU 71 (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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8B ILE* 4.1 16.4 - - + -
23B VAL* 4.0 29.8 - - + -
25B VAL* 5.3 2.5 - - + -
36B PHE* 4.1 17.0 - - + -
42B ILE* 4.3 7.9 - - + -
49B ILE* 4.2 28.3 - - + -
51B VAL* 3.6 30.7 - - + -
67B THR* 3.1 22.1 + - + +
68B ARG 3.6 5.2 - - - +
70B LEU* 1.3 73.4 - - - +
72B ALA* 1.3 67.7 + - - +
74B MET* 3.0 10.9 + - - +
75B VAL* 2.9 28.5 + - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.3 20.1 - - + +
68B ARG 2.9 14.1 + - - +
69B SER* 3.3 11.7 - - - +
71B LEU* 1.3 75.3 - - - +
73B ASN* 1.3 61.1 + - - +
75B VAL* 3.0 6.9 + - - +
76B GLU* 2.8 27.5 + - - +
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Residues in contact with ASN 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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69B SER* 2.9 25.1 + - - +
70B LEU* 3.8 10.0 - - - +
72B ALA* 1.3 76.9 - - - +
74B MET* 1.3 58.8 + - - +
76B GLU* 4.1 13.5 - - - +
77B GLY 3.0 2.6 + - - -
82B TYR* 2.4 34.1 + - + +
137B LYS* 4.4 24.2 + - + +
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Residues in contact with MET 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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23B VAL* 3.7 10.5 - - - +
25B VAL* 4.1 21.6 - - + +
32B LEU* 3.4 51.8 - - + +
34B ARG* 3.5 31.6 - - + +
36B PHE* 3.8 28.9 - - - -
70B LEU 3.0 17.8 + - - +
71B LEU* 3.0 15.3 + - - +
73B ASN* 1.3 75.7 - - - +
75B VAL* 1.3 61.6 + - - +
77B GLY 3.5 0.5 + - - -
78B VAL* 3.4 29.6 + - - +
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Residues in contact with VAL 75 (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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8B ILE* 3.8 20.4 - - + -
9B GLU 3.9 7.6 - - - +
10B ILE* 5.7 0.4 - - - -
11B PRO* 3.4 35.2 - - + -
14B VAL* 4.8 4.7 - - + -
16B VAL* 5.1 2.9 - - + -
25B VAL* 4.4 20.2 - - + -
49B ILE* 3.9 16.2 - - + -
71B LEU* 2.9 16.6 + - + +
72B ALA 3.4 8.1 - - - +
74B MET* 1.3 77.1 - - - +
76B GLU* 1.3 62.5 + - - +
78B VAL* 3.8 2.1 - - - +
79B SER* 2.9 27.7 + - - +
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Residues in contact with GLU 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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72B ALA 2.8 14.5 + - - +
73B ASN* 3.8 15.8 - - - +
75B VAL* 1.3 77.1 - - - +
77B GLY* 1.3 51.4 + - - -
79B SER* 3.7 4.9 - - - -
80B LYS* 2.7 69.4 + - + +
82B TYR* 1.8 43.7 + - + +
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Residues in contact with GLY 77 (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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29B LYS* 3.4 15.1 - - - +
73B ASN 3.0 4.3 + - - -
74B MET 3.5 1.3 + - - -
75B VAL 3.4 0.4 - - - -
76B GLU* 1.3 69.9 - - - +
78B VAL* 1.3 59.4 + - - +
79B SER 3.5 0.5 + - - -
81B GLY* 3.8 5.4 - - - -
82B TYR* 1.5 71.2 + - - -
135B ALA* 3.1 19.1 - - - +
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Residues in contact with VAL 78 (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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14B VAL* 4.2 7.4 - - + -
25B VAL* 3.6 40.4 - - + +
26B LYS 3.8 11.7 - - - +
27B GLY* 3.7 2.5 - - - +
28B PRO* 3.2 10.0 - - - +
29B LYS* 2.9 28.5 + - - -
30B GLY 3.2 34.3 - - - +
32B LEU* 4.0 18.2 - - + -
74B MET 3.4 13.5 + - - +
75B VAL 3.8 5.6 - - - +
77B GLY* 1.3 75.0 - - - +
79B SER* 1.3 60.9 + - - +
135B ALA* 4.1 1.6 - - + -
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 4.2 12.9 - - - +
12B ALA 5.8 0.7 - - - -
14B VAL* 4.1 18.8 - - - -
28B PRO* 4.1 12.6 - - - +
29B LYS* 3.4 12.1 + - - +
75B VAL* 2.9 21.7 + - - +
76B GLU* 3.3 4.9 + - - -
77B GLY 3.2 0.2 - - - -
78B VAL* 1.3 80.7 - - - +
80B LYS* 1.3 81.3 + - - +
81B GLY 3.2 9.2 + - - -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 4.0 4.8 + - - +
76B GLU* 2.7 53.0 + - + +
77B GLY 4.0 0.4 - - - -
79B SER* 1.3 82.5 + - - +
81B GLY* 1.5 61.5 + - - +
82B TYR* 4.4 2.9 - - + -
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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