Contacts of the strand formed by residues 10 - 21 (chain B) in PDB entry 3JTC
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 ARG 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.0 53.3 + - - +
9B GLN* 1.3 73.6 - - - +
11B LEU* 1.3 61.0 + - - +
12B HIS* 3.7 34.8 - - + +
32B SER 5.3 0.7 - - - +
33B LEU* 3.4 8.0 - - - +
34B GLY* 2.9 34.0 + - - +
35B GLY* 4.8 6.3 - - - +
101B CYS 3.3 14.1 - - - +
102B GLU* 3.8 27.0 + - + +
173B VAL* 3.6 9.5 - - - +
177B ILE* 4.6 0.8 - - - +
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Residues in contact with LEU 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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10B ARG* 1.3 74.3 - - - +
12B HIS* 1.3 67.4 + - - +
13B MET* 4.2 11.2 - - + -
31B ALA* 4.1 11.9 - - + -
32B SER 3.4 22.2 - - - +
33B LEU* 4.2 13.9 - - + +
38B THR* 4.8 2.5 - - - +
39B HIS* 5.2 2.0 - - + -
100B GLY* 3.1 4.7 - - - -
101B CYS 3.0 31.4 + - - -
169B CYS* 3.9 11.1 - - - -
172B TYR* 3.9 18.6 - - + -
173B VAL* 3.5 16.9 - - + +
607B PTY 3.4 45.1 - - + -
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Residues in contact with HIS 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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10B ARG* 3.7 36.6 - - + -
11B LEU* 1.3 81.5 - - - +
13B MET* 1.3 62.2 + - - +
31B ALA* 3.1 7.3 - - - +
32B SER* 2.9 35.2 + - - +
98B PHE* 3.8 20.0 - + + -
99B LEU 3.5 2.9 - - - -
101B CYS 4.3 1.6 - - - -
102B GLU* 2.6 31.2 + - - -
113B PHE* 3.6 23.4 - + - -
600B NAG 3.7 19.2 - - + +
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Residues in contact with MET 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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11B LEU* 4.2 24.0 - - + -
12B HIS* 1.3 78.1 - - - +
14B LEU* 1.3 59.8 + - - +
30B ASN 3.5 4.9 - - - -
31B ALA* 3.7 16.4 - - + -
97B CYS 3.8 0.5 - - - +
98B PHE* 3.4 7.4 - - - -
99B LEU* 2.9 67.7 + - + +
100B GLY* 4.1 19.1 - - - -
164B PHE* 3.9 24.9 - - + -
165B LEU* 5.2 0.7 - - + -
169B CYS* 4.3 5.8 - - - -
600B NAG 4.3 2.5 - - - -
607B PTY 3.7 38.1 - - + -
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Residues in contact with LEU 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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13B MET* 1.3 75.1 - - - +
15B GLN* 1.4 60.4 + - - +
16B ILE* 4.1 25.4 - - + -
29B GLY* 3.0 4.3 - - - -
30B ASN* 2.9 38.0 + - - +
96B ARG* 3.6 30.3 - - + -
97B CYS 3.4 14.1 - - - +
98B PHE* 4.0 18.4 - - + -
600B NAG 4.2 44.6 - - + +
607B PTY 3.8 5.3 - - - +
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Residues in contact with GLN 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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14B LEU* 1.4 73.9 - - - +
16B ILE* 1.3 63.8 + - - +
17B SER* 3.0 23.5 + - - +
27B TYR* 3.7 15.7 - - + -
28B GLN 3.9 2.9 - - - +
29B GLY* 4.2 1.8 - - - -
41B LEU* 5.5 4.9 - - + -
72B TYR* 2.7 32.0 + - - -
73B LEU* 3.7 11.1 - - + +
76B PHE* 3.5 25.5 - - - -
95B ILE 3.6 1.4 - - - +
96B ARG* 3.4 3.8 - - - +
97B CYS* 2.8 55.0 + - + +
99B LEU* 5.3 0.2 - - + -
607B PTY 3.9 18.9 - - + +
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Residues in contact with ILE 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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14B LEU* 4.1 26.2 - - + -
15B GLN* 1.3 76.3 - - - +
17B SER* 1.4 63.7 + - - +
18B TYR* 3.4 33.9 - - + +
26B TRP 3.8 0.9 - - - +
27B TYR* 3.4 4.3 - - - +
28B GLN* 2.7 75.1 + - + +
30B ASN* 5.5 1.8 - - - +
94B THR* 3.8 17.3 - - + -
95B ILE 3.4 4.9 - - - +
96B ARG* 4.9 9.9 - - + -
600B NAG 5.5 1.8 - - - +
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Residues in contact with SER 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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15B GLN* 3.0 30.7 + - - +
16B ILE* 1.4 72.9 - - - +
18B TYR* 1.3 61.6 + - - +
19B PHE* 3.7 14.9 - - - -
25B VAL* 3.8 1.1 - - - -
26B TRP 3.5 5.2 - - - -
27B TYR* 3.2 13.7 - - - -
76B PHE* 3.3 22.4 - - - -
94B THR* 3.4 3.6 - - - -
95B ILE* 2.8 40.8 + - - -
97B CYS* 5.8 0.2 - - - -
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Residues in contact with TYR 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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16B ILE* 3.4 27.9 - - + +
17B SER* 1.3 70.8 - - - +
19B PHE* 1.3 63.0 + - - +
20B ARG* 3.7 3.4 + - - +
25B VAL* 3.2 3.2 - - - +
26B TRP* 2.8 66.2 + + + +
28B GLN* 3.1 34.0 + - + -
93B LEU 3.8 4.0 - - - -
94B THR* 3.5 28.5 - - + -
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Residues in contact with PHE 19 (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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17B SER* 3.7 25.1 - - - -
18B TYR* 1.3 73.2 - - - +
20B ARG* 1.3 63.3 + - - +
21B ASP 3.3 12.8 - - - +
22B PRO 4.8 1.1 - - - -
24B HIS 3.5 3.4 - - - -
25B VAL* 3.7 20.9 - - + -
76B PHE* 3.8 17.9 - + - -
77B HIS* 3.6 29.8 - + - -
80B VAL* 3.8 20.9 - - + -
91B PHE* 3.6 24.3 - + + -
92B PRO* 3.2 5.7 - - - +
93B LEU* 2.8 48.9 + - + +
95B ILE* 3.7 20.0 - - + -
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Residues in contact with ARG 20 (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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18B TYR 3.7 4.2 + - - +
19B PHE* 1.3 74.4 - - - +
21B ASP* 1.3 78.5 + - - +
24B HIS* 3.3 56.0 + - + +
25B VAL* 5.8 0.9 - - - -
91B PHE* 3.7 12.8 - - - +
92B PRO* 4.1 14.8 - - + +
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Residues in contact with ASP 21 (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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19B PHE* 3.3 4.9 - - - -
20B ARG* 1.3 95.5 + - - +
22B PRO* 1.3 76.0 - - + +
23B TYR* 2.8 26.6 + - + +
24B HIS* 2.8 48.0 + - - +
91B PHE* 3.7 20.5 - - + -
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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
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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