Contacts of the helix formed by residues 5 - 19 (chain B) in PDB entry 1AN7
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 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B THR* 3.5 23.1 - - + +
4B ASP* 1.3 86.5 - - - +
6B ILE* 1.3 71.1 + - + +
8B ASP* 2.8 21.3 + - + +
9B MET* 3.2 10.0 + - - +
32B LYS* 4.4 21.3 - - - +
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Residues in contact with ILE 6 (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 ASP* 3.2 2.5 + - - +
5B PRO* 1.3 75.9 - - + +
7B ALA* 1.3 61.7 + - - +
9B MET* 3.0 12.6 + - + +
10B LEU* 3.0 30.4 + - + +
31B PHE* 3.8 26.0 - - + -
32B LYS* 4.2 22.9 - - + -
35B ILE* 3.7 25.6 - - + -
85B ARG* 3.3 41.7 - - - +
134B ILE* 3.9 15.5 - - + -
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 3.3 26.1 + - + +
5B PRO 3.3 1.0 - - - -
6B ILE* 1.3 74.1 - - - +
8B ASP* 1.3 61.2 + - - +
10B LEU* 3.9 8.1 - - - +
11B THR* 2.6 33.0 + - - +
85B ARG* 3.9 20.6 - - + +
88B LYS* 4.0 10.1 - - - +
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Residues in contact with ASP 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR* 6.4 0.9 - - + -
4B ASP 3.3 12.5 + - - +
5B PRO* 2.8 13.7 + - + +
7B ALA* 1.3 75.4 - - - +
9B MET* 1.3 61.9 + - - +
11B THR* 3.1 5.8 + - - -
12B ARG* 2.8 72.0 + - - +
26B VAL* 4.7 8.1 - - - +
27B PRO* 4.9 4.3 - - - +
32B LYS* 4.8 4.3 + - - -
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Residues in contact with MET 9 (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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5B PRO 3.2 5.8 + - - +
6B ILE* 3.0 12.7 + - + +
8B ASP* 1.3 81.7 - - - +
10B LEU* 1.3 81.8 + - + +
12B ARG* 3.3 6.1 + - - +
13B ILE* 3.0 40.1 + - + +
26B VAL* 3.5 34.1 - - + -
32B LYS* 3.9 34.1 - - + -
35B ILE* 4.1 31.2 - - + -
36B LEU* 4.4 18.2 - - + -
39B LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 10 (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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6B ILE* 3.0 26.6 + - + +
7B ALA* 4.3 4.0 - - - +
9B MET* 1.3 93.1 - - + +
11B THR* 1.3 65.5 + - - +
13B ILE* 3.0 7.1 + - + +
14B ARG* 3.0 31.9 + - - +
35B ILE* 4.8 6.7 - - + -
39B LEU* 5.1 3.6 - - + -
83B ILE* 3.6 37.0 - - + +
84B ARG* 4.1 1.1 - - - -
85B ARG* 3.6 24.9 - - + +
135B CYS* 3.5 38.1 - - + -
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Residues in contact with THR 11 (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 ALA* 2.6 22.1 + - - +
8B ASP* 3.1 4.8 + - - -
10B LEU* 1.3 75.4 - - - +
12B ARG* 1.3 57.4 + - + +
14B ARG* 3.0 35.7 + - - +
15B ASN* 2.9 52.5 + - - +
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Residues in contact with ARG 12 (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 ASP* 2.8 51.7 + - - +
9B MET* 3.7 6.7 - - - +
11B THR* 1.3 69.6 - - + +
13B ILE* 1.3 64.3 + - + +
15B ASN* 4.5 5.3 - - - +
16B ALA* 3.3 22.4 + - - +
24B THR* 3.7 18.2 + - + +
25B ASP 3.1 27.6 + - - -
26B VAL* 5.2 4.7 - - + +
27B PRO* 4.0 17.1 - - - +
58B TYR* 5.9 0.8 - - - -
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Residues in contact with ILE 13 (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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9B MET* 3.0 36.6 + - + +
10B LEU* 3.0 8.5 + - + +
12B ARG* 1.3 76.3 - - + +
14B ARG* 1.3 67.0 + - - +
16B ALA* 3.1 10.8 + - - +
17B THR* 3.2 14.8 + - - +
24B THR* 4.2 18.2 - - + -
26B VAL* 6.1 0.9 - - + -
36B LEU* 4.0 23.3 - - + -
39B LEU* 4.4 12.6 - - + -
45B ILE* 4.7 2.5 - - + -
61B VAL* 4.3 10.3 - - + -
63B LEU* 4.1 12.3 - - + -
80B ILE* 3.5 32.1 - - + -
83B ILE* 4.7 7.2 - - + -
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Residues in contact with ARG 14 (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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70A GLN* 3.4 40.3 + - - +
10B LEU* 3.0 14.0 + - - +
11B THR* 3.0 49.8 + - - +
13B ILE* 1.3 74.8 - - - +
15B ASN* 1.3 71.8 + - - +
17B THR* 2.6 25.7 + - - -
18B ARG* 3.1 35.7 + - + +
80B ILE* 5.1 1.6 - - - -
83B ILE* 3.1 36.2 + - + +
84B ARG* 4.2 10.1 - - - +
85B ARG* 5.1 2.0 - - - +
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Residues in contact with ASN 15 (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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11B THR* 2.9 38.6 + - - +
12B ARG* 4.5 4.2 - - - +
14B ARG* 1.3 85.1 + - - +
16B ALA* 1.4 61.2 + - - +
18B ARG* 3.5 14.1 + - - +
19B VAL* 3.4 18.4 + - - +
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Residues in contact with ALA 16 (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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12B ARG 3.3 17.2 + - - +
13B ILE 3.1 4.8 + - - +
15B ASN* 1.4 76.2 - - - +
17B THR* 1.3 63.4 + - - +
19B VAL* 3.0 11.4 + - - -
21B LYS* 3.1 39.6 + - + +
24B THR* 3.8 11.4 - - - +
63B LEU* 3.6 26.9 - - + -
65B TYR* 3.9 1.8 - - - -
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Residues in contact with THR 17 (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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13B ILE 3.2 10.3 + - - +
14B ARG* 2.6 20.3 + - - -
16B ALA* 1.3 80.8 - - - +
18B ARG* 1.3 74.1 + - - +
20B TYR* 2.8 18.7 + - - -
63B LEU* 3.8 24.9 - - + -
64B LYS 5.0 4.0 - - - +
65B TYR* 3.1 14.1 - - + +
78B GLN* 3.0 38.2 + - - +
80B ILE* 4.6 16.2 - - + -
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Residues in contact with ARG 18 (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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69A ARG* 6.1 4.0 - - - +
14B ARG* 3.1 33.9 + - + +
15B ASN* 4.0 8.7 - - - +
16B ALA 3.2 1.0 - - - -
17B THR* 1.3 100.9 + - - +
19B VAL* 1.3 65.4 + - + +
20B TYR* 3.5 12.3 - - - -
78B GLN* 3.3 27.8 + - - +
80B ILE* 2.8 48.2 + - - +
81B HIS* 4.0 13.3 + - - +
82B HIS* 5.1 1.0 - - - +
83B ILE* 5.3 0.2 - - - +
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN 3.4 12.5 + - - +
16B ALA* 3.4 10.3 - - - +
17B THR 3.0 0.6 - - - -
18B ARG* 1.3 83.1 - - + +
20B TYR* 1.3 73.8 + - - +
21B LYS* 3.2 21.3 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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