Contacts of the helix formed by residues 57 - 75 (chain B) in PDB entry 1C7C
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 ASN 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE 2.9 24.2 + - - +
47B ASP* 3.2 26.0 + - - +
48B LEU* 3.9 5.1 - - - +
53B ALA 3.0 10.8 + - - +
54B VAL* 3.1 15.1 + - - +
56B GLY* 1.3 75.1 - - - +
58B PRO* 1.3 70.3 - - - +
59B LYS* 2.7 36.0 + - - +
60B VAL* 3.1 19.8 + - + +
61B LYS* 3.1 24.2 + - - +
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Residues in contact with PRO 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 3.3 9.1 - - - +
57B ASN* 1.3 89.1 - - - +
59B LYS* 1.3 62.8 + - + +
61B LYS* 3.6 11.0 + - + +
62B ALA* 3.0 27.7 + - - +
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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
----------------------------------------------------------
44B SER* 2.6 33.1 + - - -
45B PHE* 3.4 51.3 - - + +
57B ASN* 2.7 17.2 + - - +
58B PRO* 1.3 75.8 - - + +
60B VAL* 1.3 62.5 + - - +
62B ALA* 3.3 6.0 + - - +
63B HIS* 3.0 19.2 + - - +
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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
----------------------------------------------------------
25B GLY* 4.6 3.1 - - - +
28B LEU* 3.6 11.0 - - + +
29B GLY* 4.0 28.9 - - - +
32B LEU* 3.8 27.6 - - + -
45B PHE* 3.9 17.7 - - + -
48B LEU* 3.9 10.8 - - + -
54B VAL* 3.9 12.8 - - + +
55B MET* 5.7 0.4 - - - -
57B ASN* 3.1 30.2 + - + +
59B LYS* 1.3 73.9 - - - +
61B LYS* 1.3 69.4 + - + +
63B HIS 3.3 0.9 + - - -
64B GLY* 2.9 20.3 + - - -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP 4.8 11.9 + - - +
22B GLU* 5.4 5.1 - - - +
25B GLY* 4.1 24.3 + - - +
55B MET 4.0 19.5 - - - +
56B GLY* 4.8 5.4 - - - +
57B ASN 3.1 16.3 + - - +
58B PRO* 3.9 9.6 - - + +
60B VAL* 1.3 77.6 - - + +
62B ALA* 1.3 62.6 + - - +
64B GLY* 3.3 2.1 + - - -
65B LYS* 3.0 22.9 + - - +
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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
----------------------------------------------------------
58B PRO 3.0 18.6 + - - +
59B LYS* 3.8 6.7 - - - +
60B VAL 3.2 0.2 - - - -
61B LYS* 1.3 76.9 - - - +
63B HIS* 1.3 62.2 + - - +
65B LYS* 3.4 14.1 + - + +
66B LYS* 3.1 25.1 + - - +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.5 28.3 - - + -
42B PHE* 3.6 17.7 - + - -
45B PHE* 3.8 13.9 - + + -
59B LYS 3.0 17.2 + - - +
62B ALA* 1.3 76.0 - - - +
64B GLY* 1.3 59.8 + - - +
66B LYS* 3.1 18.9 + - + +
67B VAL* 2.9 46.5 + - + +
147B HEM 3.3 71.9 + + + +
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 3.3 38.3 - - - +
28B LEU* 3.6 11.8 - - - +
60B VAL 2.9 15.5 + - - -
61B LYS 3.6 2.7 - - - -
63B HIS* 1.3 76.9 - - - +
65B LYS* 1.3 54.7 + - - +
67B VAL* 3.5 4.5 + - - +
68B LEU* 2.9 24.6 + - - +
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.5 3.9 - - - +
21B ASP* 2.5 66.6 + - - +
24B GLY* 4.3 1.9 - - - -
61B LYS 3.0 12.1 + - - +
62B ALA* 3.6 13.9 - - + +
63B HIS 3.2 0.2 - - - -
64B GLY* 1.3 76.5 - - - +
66B LYS* 1.3 60.6 + - - +
68B LEU* 4.5 0.2 - - - +
69B GLY* 2.9 26.7 + - - -
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 3.1 14.2 + - - +
63B HIS* 3.1 25.9 + - - +
65B LYS* 1.3 78.0 - - - +
67B VAL* 1.3 65.5 + - - +
69B GLY* 3.4 1.4 + - - -
70B ALA* 3.2 22.9 + - - +
147B HEM 3.8 63.2 + - + +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 5.2 6.1 - - + -
63B HIS* 2.9 48.9 + - + +
64B GLY* 3.9 5.4 - - - +
66B LYS* 1.3 76.2 - - - +
68B LEU* 1.3 65.9 + - + +
70B ALA* 3.2 5.5 + - - +
71B PHE* 3.0 23.6 + - - +
106B LEU* 3.8 19.7 - - + -
147B HEM 3.6 55.2 - - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.8 23.3 - - + -
20B VAL* 3.8 16.1 - - + +
23B VAL* 3.5 20.4 - - + -
24B GLY* 3.4 32.1 - - - +
27B ALA* 4.8 7.2 - - + -
64B GLY 2.9 17.2 + - - +
67B VAL* 1.3 82.6 - - + +
69B GLY* 1.3 61.1 + - - +
71B PHE* 3.5 10.9 - - + +
72B SER* 2.8 30.5 + - - -
106B LEU* 5.7 5.6 - - + -
110B LEU* 4.2 27.6 - - + -
147B HEM 6.3 0.7 - - + -
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.9 10.5 - - - +
65B LYS 2.9 19.2 + - - -
66B LYS 3.4 1.8 + - - -
67B VAL 3.2 0.4 - - - -
68B LEU* 1.3 79.1 - - - +
70B ALA* 1.3 56.3 + - - +
72B SER* 3.4 3.7 + - - -
73B ASP* 3.0 35.3 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS 3.2 5.6 + - - +
67B VAL 3.6 7.6 - - - +
69B GLY* 1.3 73.9 - - - +
71B PHE* 1.3 65.1 + - - +
73B ASP* 3.4 6.8 + - - +
74B GLY* 3.0 16.1 + - - -
85B PHE* 3.8 10.8 - - + -
88B LEU* 4.4 9.2 - - + -
147B HEM 3.7 43.3 - - + -
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.7 36.6 - + - -
67B VAL 3.0 13.2 + - - +
68B LEU* 3.5 17.5 - - + +
70B ALA* 1.3 76.6 - - - +
72B SER* 1.3 58.2 + - - +
74B GLY* 2.9 18.2 + - - -
75B LEU* 3.2 26.9 + - + +
85B PHE* 4.6 5.0 - - - -
110B LEU* 3.8 24.7 - - + -
130B TYR* 5.2 6.1 - + - -
133B VAL* 4.2 17.9 - - + -
134B VAL* 4.3 15.3 - - + -
137B VAL* 3.9 38.6 - - + +
147B HEM 4.1 20.3 - - + +
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 2.9 37.5 + - - +
20B VAL* 4.1 11.5 - - - +
68B LEU 2.8 18.3 + - - -
69B GLY* 3.5 8.3 - - - -
71B PHE* 1.3 77.0 - - - +
73B ASP* 1.3 67.9 + - - +
75B LEU* 3.1 20.8 + - - +
76B ALA* 4.0 2.8 + - - +
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 3.0 22.5 + - - +
70B ALA* 4.1 5.8 - - - +
72B SER* 1.3 80.5 + - - +
74B GLY* 1.3 61.6 + - - +
75B LEU 3.3 0.3 + - - -
76B ALA* 3.3 14.6 + - - +
77B HIS* 3.4 19.1 + - + -
84B THR* 5.5 1.6 - - - -
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Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA 3.0 10.4 + - - -
71B PHE 2.9 11.7 + - - -
73B ASP* 1.3 78.3 - - - +
75B LEU* 1.3 57.0 + - - +
76B ALA 3.1 1.1 - - - -
77B HIS* 2.9 27.4 + - - +
81B LEU* 3.7 12.1 - - - +
84B THR* 4.4 10.1 - - - -
85B PHE* 3.9 20.2 - - - -
137B VAL* 6.3 1.1 - - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 4.5 17.3 - - + -
12B THR* 5.3 4.4 + - - -
15B TRP* 3.5 51.4 - - + +
71B PHE* 3.2 28.0 + - + +
72B SER 3.1 8.7 + - - +
74B GLY* 1.3 77.8 - - - +
76B ALA* 1.3 58.4 + - - +
77B HIS 3.1 1.7 + - - -
78B LEU* 3.5 30.6 - - + +
130B TYR* 5.0 1.1 - - + +
133B VAL* 3.7 30.3 - - + -
137B VAL* 5.6 2.2 - - + -
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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