Contacts of the strand formed by residues 24 - 33 (chain A) 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 HIS 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.6 1.7 - - - -
20A ARG* 3.3 34.8 + - + +
21A ASP* 2.9 37.9 + - - +
22A PRO 3.6 0.8 + - - -
23A TYR* 1.3 98.6 + + + +
25A VAL* 1.3 62.5 + - - +
45A ASP* 3.5 8.1 - - - +
46A THR* 6.3 2.2 - - + -
106B GLU* 3.0 31.6 + - + +
107B GLY* 4.7 9.8 + - - -
108B SER* 5.5 0.7 - - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.7 18.6 - - - -
18A TYR 3.2 13.0 - - - +
19A PHE* 3.8 17.9 - - + -
20A ARG* 6.2 0.4 - - - -
24A HIS* 1.3 76.5 - - - +
26A TRP* 1.3 65.2 + - - +
27A TYR* 3.6 38.6 - - + +
44A PRO* 3.5 5.0 - - - +
45A ASP* 3.0 51.7 + - + +
77A HIS* 4.0 13.9 - - + +
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Residues in contact with TRP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.5 1.2 - - - -
18A TYR* 2.8 63.1 + + + +
25A VAL* 1.3 74.2 - - - +
27A TYR* 1.3 70.4 + - - +
28A GLN* 4.6 1.5 - - - +
42A GLU* 2.8 43.8 + - + +
43A GLY* 3.6 15.5 - - - -
44A PRO* 3.6 35.4 - - + -
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 3.7 17.9 - - + -
16A ILE 3.4 2.2 - - - +
17A SER* 3.2 29.2 - - - -
25A VAL* 3.6 28.9 - - + +
26A TRP* 1.3 80.4 - - - +
28A GLN* 1.3 63.1 + - - +
41A LEU* 3.7 17.5 - - + -
42A GLU* 3.2 3.4 - - - -
43A GLY 2.9 34.2 + - - +
45A ASP* 3.9 16.5 - - + +
48A THR* 3.4 21.8 - - + -
73A LEU* 3.2 46.7 + - + -
76A PHE* 3.9 6.0 - + - -
77A HIS* 3.5 17.8 + - - +
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Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 4.6 0.2 - - - -
16A ILE 2.7 38.2 + - - +
18A TYR* 3.4 33.5 + - + -
26A TRP* 4.6 2.0 - - + +
27A TYR* 1.3 77.7 - - - +
29A GLY* 1.3 57.9 + - - +
41A LEU* 3.4 8.3 - - - -
42A GLU* 3.0 33.5 + - - +
603A NAG 3.4 37.1 + - - -
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 2.9 16.6 - - - -
15A GLN* 4.1 2.0 - - - -
28A GLN* 1.3 75.9 - - - +
30A ASN* 1.3 70.1 + - - +
40A VAL* 3.6 2.9 - - - +
41A LEU* 2.8 41.8 + - - +
603A NAG 4.2 4.5 - - - -
606A PTY 4.8 1.3 - - - -
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Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A MET* 3.4 1.0 - - - -
14A LEU* 2.8 38.3 + - - +
28A GLN* 6.1 0.2 - - - +
29A GLY* 1.3 75.2 + - - +
31A ALA* 1.3 66.1 + - - +
32A SER* 5.2 1.7 + - - -
37A LEU* 3.9 14.4 - - + +
39A HIS 3.1 17.9 - - - +
40A VAL* 4.3 5.6 - - + -
603A NAG 1.4 64.8 + - - +
606A PTY 3.6 11.7 - - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.3 6.1 - - + -
12A HIS 3.1 13.7 - - - +
13A MET* 3.8 16.2 - - + -
30A ASN* 1.3 77.9 - - - +
32A SER* 1.3 64.5 + - - +
37A LEU* 3.5 4.3 - - - +
38A THR* 2.9 24.9 + - - +
39A HIS* 3.0 30.4 + - + +
606A PTY 3.8 11.2 - - + -
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.9 1.0 - - - +
11A LEU* 3.4 8.5 - - - +
12A HIS* 2.9 38.0 + - - +
30A ASN* 5.2 1.9 + - - -
31A ALA* 1.3 75.5 + - - +
33A LEU* 1.3 59.7 + - - +
34A GLY 3.7 16.1 + - - +
35A GLY 4.8 1.7 + - - -
36A HIS 3.2 12.3 - - - -
37A LEU* 3.5 19.9 + - - +
38A THR* 3.7 2.0 - - - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG 3.4 12.3 - - - +
11A LEU* 3.9 24.0 - - + -
32A SER* 1.3 69.7 - - - +
34A GLY* 1.3 65.3 + - - +
35A GLY 3.3 0.3 + - - -
36A HIS* 2.9 26.2 + - + +
38A THR* 3.9 23.5 - - + +
56A LEU* 4.3 7.6 - - + -
172A TYR* 4.0 25.8 - - + -
173A VAL* 4.2 12.8 - - + -
176A HIS* 4.0 27.1 - - + +
177A ILE* 3.9 25.0 - - + +
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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