Contacts of the helix formed by residues 13 - 34 (chain J) in PDB entry 6CP3
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 13 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248 LEU* 3.6 41.1 - - + -
288 SER* 6.0 0.2 - - - -
8J PRO 5.1 3.4 - - - -
9J ILE* 3.3 27.1 + - + +
12J VAL* 1.3 89.9 - - + +
14J TRP* 1.3 64.2 + - - +
15J PRO* 3.6 4.7 - - - -
16J PHE* 4.2 10.2 + + + +
17J PHE* 4.0 14.7 + - - +
84X LEU 2.9 20.5 + - - -
85X TYR* 3.3 35.5 - + - -
87X PRO* 3.3 14.9 - - + +
88X MET* 3.0 47.3 + - + -
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Residues in contact with TRP 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J LEU* 3.7 30.5 + - + +
11J LYS* 3.2 24.9 - - - -
12J VAL* 3.4 19.2 - - - -
13J TYR* 1.3 76.0 - - - +
15J PRO* 1.4 90.3 - - + +
17J PHE* 3.1 9.7 + - - +
18J VAL* 2.9 37.8 + - + +
131X ILE* 5.3 5.9 + - + +
132X LEU* 4.8 13.2 - - + +
135X TYR* 3.9 39.3 - + + +
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Residues in contact with PRO 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J VAL 4.0 7.2 - - - +
13J TYR* 3.6 4.0 - - - -
14J TRP* 1.4 109.3 - - + +
16J PHE* 1.3 67.2 + - + +
18J VAL* 3.3 9.4 + - + +
19J ALA* 2.8 28.6 + - - +
128X GLY* 3.6 25.0 - - - +
131X ILE* 3.7 22.7 - - + +
132X LEU* 3.8 26.2 - - + +
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Residues in contact with PHE 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J TYR* 4.2 13.0 + + + +
14J TRP 3.3 0.8 - - - -
15J PRO* 1.3 85.1 - - + +
17J PHE* 1.3 60.9 + - - +
19J ALA* 3.5 1.5 + - - +
20J GLY* 2.9 22.7 + - - -
85X TYR* 4.8 4.9 - + - -
88X MET* 3.6 43.1 - - + -
124X VAL* 3.4 15.0 - - + +
125X ILE* 3.1 44.4 - - + -
128X GLY* 3.7 11.0 - - - -
129X ASN* 3.2 30.1 - - - -
132X LEU* 4.3 20.2 - - + -
242X LEU* 4.8 0.9 - - + -
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Residues in contact with PHE 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218 ILE* 3.6 41.1 - - + -
10J LEU* 6.2 3.8 - - + -
13J TYR 4.0 9.7 + - - +
14J TRP* 3.1 11.0 + - - +
16J PHE* 1.3 77.0 - - - +
18J VAL* 1.3 64.1 + - + +
20J GLY* 3.3 2.2 + - - +
21J ALA* 3.0 34.8 + - + +
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Residues in contact with VAL 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J TRP* 2.9 31.8 + - + +
15J PRO* 3.5 12.8 - - + +
17J PHE* 1.3 80.9 - - + +
19J ALA* 1.3 57.6 + - - +
21J ALA* 3.2 8.1 + - - +
22J ALA* 2.9 28.0 + - + +
131X ILE* 5.1 16.2 - - + -
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Residues in contact with ALA 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PRO 2.8 17.2 + - - +
16J PHE 3.8 2.2 - - - +
17J PHE 3.3 0.2 - - - -
18J VAL* 1.3 74.0 - - - +
20J GLY* 1.3 59.8 + - - +
22J ALA* 3.7 7.5 - - - +
23J VAL* 2.9 34.5 + - - +
124X VAL* 3.3 29.4 - - - +
127X LEU* 3.7 15.0 - - + -
128X GLY 3.5 11.2 - - - +
131X ILE* 5.7 2.5 - - + -
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Residues in contact with GLY 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178 PHE* 3.8 17.6 - - - -
16J PHE 2.9 16.1 + - - -
17J PHE* 3.3 5.1 + - - -
19J ALA* 1.3 76.6 - - - +
21J ALA* 1.3 55.7 + - - +
23J VAL 3.5 0.5 + - - -
24J TYR* 2.9 28.6 + - - +
124X VAL* 3.6 18.8 - - - +
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J PHE* 3.0 21.4 + - + +
18J VAL* 3.5 10.3 - - - +
20J GLY* 1.3 76.5 - - - +
22J ALA* 1.3 57.9 + - - +
24J TYR* 3.3 9.4 + - - +
25J TYR* 3.0 28.9 + - - +
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Residues in contact with ALA 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J VAL* 2.9 17.7 + - + +
19J ALA* 3.7 8.7 - - - +
20J GLY 3.3 0.2 - - - -
21J ALA* 1.3 78.0 - - - +
23J VAL* 1.3 58.3 + - + +
25J TYR* 3.3 5.4 + - - +
26J GLY* 2.9 25.8 + - - -
127X LEU* 5.5 6.3 - - + -
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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
----------------------------------------------------------
138 LEU* 4.9 3.4 - - + -
178 PHE* 4.6 3.4 - - + -
19J ALA 2.9 21.3 + - - +
20J GLY 4.0 1.1 - - - +
22J ALA* 1.3 72.8 - - - +
24J TYR* 1.3 60.3 + - - +
26J GLY* 4.4 1.8 - - - +
27J MET* 2.8 36.5 + - + +
120X SER* 3.5 28.7 - - - +
123X ILE* 3.7 29.6 - - + -
124X VAL* 3.7 19.5 - - + +
127X LEU* 4.0 13.9 - - + -
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Residues in contact with TYR 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108 MET* 4.0 19.1 - - + +
138 LEU* 3.6 24.5 - - + -
148 THR* 3.5 28.9 + - + +
178 PHE* 4.7 6.0 - + + -
20J GLY 2.9 20.2 + - - +
21J ALA* 3.5 9.6 - - - +
22J ALA 3.3 0.2 - - - -
23J VAL* 1.3 76.4 - - - +
25J TYR* 1.3 61.5 + + + +
27J MET* 3.3 6.0 + - - +
28J SER* 2.9 29.9 + - - -
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Residues in contact with TYR 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ALA 3.0 15.8 + - - +
22J ALA* 3.9 6.1 - - - +
24J TYR* 1.3 78.7 - + + +
26J GLY* 1.3 60.6 + - - +
28J SER* 3.2 15.2 + - - -
29J LYS* 3.0 59.9 + - + +
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Residues in contact with GLY 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J ALA 2.9 16.4 + - - -
23J VAL* 3.7 2.2 - - - -
25J TYR* 1.3 77.8 - - - +
27J MET* 1.3 56.3 + - - +
29J LYS* 3.3 12.8 + - - +
30J ALA* 2.9 27.4 + - - +
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Residues in contact with MET 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 PHE* 4.5 24.9 - - + -
108 MET* 3.4 17.4 - - + +
138 LEU* 3.8 31.6 - - + -
23J VAL* 2.8 25.5 + - + +
24J TYR* 3.6 5.4 - - - +
26J GLY* 1.3 73.8 - - - +
28J SER* 1.3 61.5 + - - +
30J ALA* 4.1 12.8 - - + -
31J ALA* 2.8 33.2 + - + +
116X VAL* 4.6 16.4 - - + -
120X SER* 4.7 8.7 - - - +
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Residues in contact with SER 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108 MET* 3.5 12.3 - - - +
24J TYR* 2.9 19.7 + - - -
25J TYR* 3.3 24.1 - - - -
27J MET* 1.3 76.8 - - - +
29J LYS* 1.3 56.5 + - - +
32J ASP* 2.9 49.3 + - - +
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Residues in contact with LYS 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J TYR* 3.0 52.2 + - + +
26J GLY* 3.3 12.5 + - - +
28J SER* 1.3 74.6 - - - +
30J ALA* 1.3 57.2 + - - +
32J ASP* 3.5 4.4 + - - +
33J LEU* 2.9 35.4 + - + +
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J GLY 2.9 16.5 + - - +
27J MET* 3.8 18.4 - - + +
28J SER 3.3 0.4 - - - -
29J LYS* 1.3 77.4 - - - +
31J ALA* 1.3 52.0 + - - +
32J ASP 3.2 0.2 - - - -
33J LEU* 3.0 3.8 + - - -
34J SER* 2.5 49.7 + - - +
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Residues in contact with ALA 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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78 PHE 6.1 0.9 - - - +
98 PHE* 5.5 10.5 - - + -
108 MET* 4.3 21.5 - - + -
27J MET* 2.8 26.9 + - + +
28J SER 4.5 0.2 - - - +
30J ALA* 1.3 71.8 - - - +
32J ASP* 1.3 64.1 + - - +
34J SER* 4.3 4.0 - - - +
35J SER* 2.9 29.3 + - - -
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Residues in contact with ASP 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J SER* 2.9 33.8 + - - +
29J LYS* 4.0 4.4 - - - +
31J ALA* 1.3 82.7 - - - +
33J LEU* 1.3 56.8 + - - +
34J SER 3.7 0.4 - - - -
35J SER* 4.4 4.3 + - - -
36J ASN* 4.3 13.2 + - - -
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Residues in contact with LEU 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J LYS* 2.9 20.0 + - + +
30J ALA* 3.8 2.9 - - - +
32J ASP* 1.3 79.4 - - - +
34J SER* 1.3 62.5 + - - +
35J SER 3.6 1.5 + - - -
36J ASN* 4.7 10.7 + - - +
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Residues in contact with SER 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 PHE* 6.0 2.3 - - - -
30J ALA* 2.5 35.1 + - - +
31J ALA* 4.3 2.7 - - - -
33J LEU* 1.3 80.2 - - - +
35J SER* 1.3 57.0 + - - +
36J ASN 3.5 2.7 - - - +
37J THR* 4.4 14.5 - - - +
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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