Contacts of the helix formed by residues 15 - 33 (chain J) in PDB entry 3AOI
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 SER 15 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1213I ARG* 3.9 5.6 - - - +
1216I SER* 2.9 22.1 - - - -
1217I ILE* 2.6 35.1 + - - -
1480I PHE* 4.2 10.5 - - - -
1481I VAL* 5.1 0.7 - - - -
13J VAL* 3.0 15.0 - - - +
14J ASP* 1.3 91.5 - - - +
16J LYS* 1.3 68.1 + - - +
17J TYR 4.2 2.8 + - - -
18J ARG* 3.2 19.3 + - - +
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Residues in contact with LYS 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043H TYR 5.6 0.7 - - - +
710I ARG* 4.8 7.6 - - - +
761I ILE* 5.7 1.0 - - + +
762I GLN* 4.4 25.7 + - + +
767I HIS 5.7 1.6 + - - -
768I ASN* 4.5 7.3 + - - -
1209I LEU* 2.8 45.7 - - + +
1210I SER* 4.1 14.5 + - - -
1211I MET* 5.4 0.4 - - - +
1213I ARG* 3.8 4.8 - - - +
1216I SER* 2.4 37.4 + - - +
1219I GLU* 4.3 0.9 - - - +
10J PHE* 3.7 39.8 - - + -
15J SER* 1.3 63.5 - - - +
17J TYR* 1.3 76.1 + - + +
18J ARG 2.8 0.5 + - - -
19J LEU* 2.7 36.2 + - - +
20J THR* 3.7 2.9 + - + +
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Residues in contact with TYR 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042H ALA 4.0 10.0 + - - -
1043H TYR 3.5 11.5 + - - -
1044H GLY* 3.6 9.9 - - - -
710I ARG* 4.7 1.6 + - - -
762I GLN* 3.5 24.7 - - - -
1216I SER* 4.0 12.1 - - - -
1217I ILE 3.6 11.7 - - - +
1218I GLY 3.2 28.3 - - - -
1219I GLU* 2.5 46.6 + - + +
1220I ALA 4.2 0.2 + - - -
1475I GLY* 3.3 31.2 - - - +
1476I THR* 4.0 4.0 - - - -
1478I SER* 4.3 7.0 - - - +
1481I VAL* 4.5 2.5 - - + -
15J SER* 4.8 0.2 - - - +
16J LYS* 1.3 85.6 - - + +
18J ARG* 1.3 62.4 + - - +
20J THR* 2.5 24.2 + - - +
21J VAL* 3.1 13.4 - - - +
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Residues in contact with ARG 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1480I PHE* 4.1 22.1 + - - -
1481I VAL* 3.2 45.2 - - + +
1483I PHE 6.0 0.2 - - - -
1484I THR* 3.7 25.8 + - - +
13J VAL* 3.8 20.6 - - + -
14J ASP* 3.5 31.5 + - - +
15J SER* 3.2 18.1 + - - +
16J LYS 2.8 4.8 + - - -
17J TYR* 1.3 73.8 - - - +
19J LEU* 1.3 65.0 + - - +
21J VAL* 3.0 15.4 + - - +
22J VAL* 3.1 15.2 + - + +
75J PHE* 5.5 6.5 - - + -
76J GLY* 5.6 2.6 - - - -
77J GLU* 4.7 18.8 - - - +
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Residues in contact with LEU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761I ILE* 4.7 6.5 - - + -
6J ILE* 3.8 11.0 - - + -
9J LEU* 3.3 45.1 - - + +
10J PHE* 3.7 27.6 - - + +
12J MET* 6.5 0.2 - - + -
13J VAL* 3.9 25.1 - - + +
15J SER 3.6 1.0 + - - -
16J LYS 2.7 17.4 + - - +
18J ARG* 1.3 74.5 - - - +
20J THR* 1.3 58.3 + - - +
22J VAL* 3.2 4.1 + - + +
23J VAL* 2.8 61.5 + - + +
68J LEU* 4.2 8.3 - - + -
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Residues in contact with THR 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754I PHE* 4.4 2.7 - - - -
757I ALA* 4.3 2.4 - - - +
758I GLU* 3.6 12.6 - - - +
761I ILE* 3.2 39.7 - - + -
762I GLN* 2.5 36.8 + - + +
1476I THR* 3.8 5.8 + - - -
16J LYS 3.7 1.7 + - - +
17J TYR* 2.5 26.7 + - - -
19J LEU* 1.3 76.9 - - - +
21J VAL* 1.3 49.9 + - - +
23J VAL* 3.1 8.0 + - - +
24J ALA* 2.7 38.8 + - - +
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Residues in contact with VAL 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754I PHE* 3.4 25.5 - - + -
1476I THR* 3.3 24.7 - - + +
1481I VAL* 3.2 39.9 - - + +
1482I ARG* 4.6 7.9 - - - +
1484I THR* 4.4 5.2 - - - +
17J TYR 3.1 18.2 - - - +
18J ARG 3.0 3.3 + - - +
20J THR* 1.3 72.8 - - - +
22J VAL* 1.3 64.7 + - - +
24J ALA* 3.2 1.0 + - - +
25J LYS* 3.0 38.5 + - + +
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Residues in contact with VAL 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484I THR* 3.5 30.3 - - + -
1486I VAL* 3.5 23.6 - - + +
13J VAL* 5.5 2.2 - - + -
18J ARG* 3.1 18.9 + - + +
19J LEU* 3.5 9.6 - - + +
21J VAL* 1.3 80.9 - - - +
23J VAL* 1.3 66.6 + - - +
24J ALA 3.0 1.0 + - - -
25J LYS* 3.5 2.4 + - - +
26J ARG* 3.0 22.6 + - + +
68J LEU* 3.4 28.3 - - + -
73J LEU* 6.1 0.4 - - + -
75J PHE* 3.8 24.9 - - + -
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Residues in contact with VAL 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757I ALA* 4.8 5.6 - - + -
761I ILE* 4.5 9.0 - - + -
19J LEU* 2.8 51.5 + - + +
20J THR* 3.5 6.1 - - - +
22J VAL* 1.3 72.7 - - - +
24J ALA* 1.3 65.2 + - - +
26J ARG* 3.5 0.4 - - - +
27J ALA* 3.2 13.5 + - - +
61J VAL* 4.3 9.6 - - + +
64J ALA* 3.4 19.1 - - + +
65J MET* 3.3 37.7 - - + -
68J LEU* 3.6 16.4 - - + -
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Residues in contact with ALA 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753I SER* 4.5 4.9 - - - -
754I PHE* 3.3 46.7 - - + -
757I ALA* 3.9 10.3 - - + +
20J THR 2.7 21.2 + - - +
21J VAL 3.4 3.6 - - - +
22J VAL 3.0 0.6 + - - -
23J VAL* 1.3 67.5 - - - +
25J LYS* 1.3 55.2 + - - +
26J ARG 2.6 3.8 + - - -
27J ALA* 2.4 35.1 + - - +
28J GLN* 3.2 10.2 + - - +
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Residues in contact with LYS 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754I PHE* 4.1 11.0 - - + -
1482I ARG 5.4 3.7 + - - +
1483I PHE* 5.8 0.6 - - - +
1484I THR 2.8 33.5 + - - +
1485I GLN* 4.3 11.2 + - - +
1486I VAL* 4.5 12.1 - - + +
21J VAL* 3.0 28.2 + - + +
22J VAL* 4.1 2.9 - - - +
24J ALA* 1.3 75.7 - - - +
26J ARG* 1.3 61.0 + - - +
28J GLN* 3.0 39.5 + - - +
29J GLN* 3.0 24.0 - - + +
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Residues in contact with ARG 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486I VAL* 4.1 9.5 - - + +
1487I VAL 5.9 0.4 - - - -
1488I ASP* 5.4 4.9 + - - +
22J VAL 3.0 18.6 + - - +
23J VAL* 3.5 4.7 - - - +
24J ALA 2.6 4.9 + - - -
25J LYS* 1.3 74.4 - - - +
27J ALA* 1.3 62.8 + - - +
29J GLN* 3.2 23.9 + - - +
30J LEU* 3.0 38.0 + - + +
37J ASN 2.9 27.4 + - - -
38J THR* 3.5 0.6 - - - +
39J VAL* 5.0 1.6 - - - +
64J ALA* 3.5 23.1 - - + -
67J GLU* 2.5 43.9 + - - -
68J LEU* 4.3 8.7 - - + -
73J LEU* 3.1 39.8 - - - +
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Residues in contact with ALA 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075H ASP* 4.7 0.7 - - - -
753I SER* 4.4 10.1 - - - -
23J VAL 3.2 9.0 + - - +
24J ALA* 2.4 25.0 + - - +
26J ARG* 1.3 72.9 - - - +
28J GLN* 1.3 62.1 + - - +
30J LEU* 3.2 26.3 + - - +
31J LEU* 3.4 13.5 + - - +
60J ALA* 3.7 21.9 - - + +
61J VAL* 3.8 23.3 - - + +
64J ALA* 4.7 0.2 - - + -
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Residues in contact with GLN 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075H ASP* 3.4 16.6 - - - +
1078H GLU* 4.9 11.3 + - - +
753I SER* 5.1 5.6 - - - -
754I PHE* 3.6 23.1 - - - +
24J ALA 3.2 4.7 + - - +
25J LYS* 3.0 44.3 + - - +
27J ALA* 1.3 77.7 - - - +
29J GLN* 1.3 60.4 + - + +
31J LEU* 3.0 8.1 + - - +
32J ARG* 2.9 58.6 + - - +
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Residues in contact with GLN 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486I VAL* 3.1 49.5 + - - +
1487I VAL* 5.4 0.9 - - - -
25J LYS* 3.0 19.5 + - - +
26J ARG* 3.5 22.8 + - - +
28J GLN* 1.3 78.1 - - + +
30J LEU* 1.3 63.0 + - - +
31J LEU 3.2 0.5 + - - -
32J ARG* 4.1 2.9 - - - +
33J HIS* 3.6 31.5 + - + +
34J GLY 3.8 4.5 - - - +
37J ASN* 4.4 7.1 - - + +
73J LEU* 5.5 0.2 - - - +
85J LEU* 4.2 12.3 - - - +
89J MET* 3.6 30.9 - - + +
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Residues in contact with LEU 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ARG* 3.0 63.7 + - + +
27J ALA* 3.3 18.6 - - - +
28J GLN 3.1 0.6 - - - -
29J GLN* 1.3 77.9 - - - +
31J LEU* 1.3 55.2 + - - +
34J GLY 2.6 21.0 - - - +
35J PHE* 3.0 36.4 - - + +
37J ASN* 4.6 8.7 - - - +
38J THR* 4.7 3.4 - - - -
60J ALA* 4.1 7.6 - - + +
63J TRP* 4.0 24.9 - - + -
64J ALA 3.9 12.8 - - - +
67J GLU* 3.5 9.4 - - - +
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Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073H GLY 5.9 0.9 - - - +
1074H GLU* 4.9 7.6 - - + +
1075H ASP* 2.6 57.7 - - + +
753I SER* 3.9 9.4 - - - +
27J ALA 3.4 10.3 - - - +
28J GLN 3.0 8.7 - - - +
30J LEU* 1.3 80.3 - - - +
32J ARG* 1.3 89.9 + - + +
33J HIS 3.6 0.4 - - - -
34J GLY* 3.3 11.5 + - - -
35J PHE* 4.0 17.2 + - + -
60J ALA* 4.7 9.4 - - + -
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Residues in contact with ARG 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075H ASP* 4.8 13.4 + - - +
1076H VAL 5.6 2.8 + - - -
1078H GLU* 5.8 7.1 - - - +
28J GLN* 2.9 56.9 + - - +
29J GLN* 4.1 1.6 - - - +
31J LEU* 1.3 87.8 - - + +
33J HIS* 1.3 86.5 + - + +
34J GLY 2.9 6.1 + - - -
86J GLN* 6.0 3.6 - - - +
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Residues in contact with HIS 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLN* 3.6 19.2 + - + +
32J ARG* 1.3 97.9 - - + +
34J GLY* 1.3 59.5 + - - +
37J ASN* 3.0 29.1 + - - +
85J LEU* 5.2 3.2 - - - +
86J GLN* 4.2 25.0 - - + +
89J MET* 3.2 54.6 - - + +
90J GLU* 4.1 17.9 - - + +
93J TYR* 3.5 19.8 - - - +
94J PRO 4.9 1.7 - - - -
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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