Contacts of the strand formed by residues 24 - 33 (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 HIS 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.5 3.9 - - - -
20B ARG* 3.3 66.7 + - + +
21B ASP* 2.8 38.0 + - - +
22B PRO 3.5 1.0 - - - -
23B TYR* 1.3 97.7 + + + +
25B VAL* 1.3 60.3 + - - +
45B ASP* 3.3 10.3 - - - +
46B THR* 5.9 5.8 - - + -
77B HIS* 4.6 0.2 - - - -
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Residues in contact with VAL 25 (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* 3.8 11.4 - - - -
18B TYR 3.2 11.2 - - - +
19B PHE* 3.7 27.6 - - + -
20B ARG* 5.8 0.9 - - - -
24B HIS* 1.3 76.3 - - - +
26B TRP* 1.3 64.3 + - - +
27B TYR* 3.4 41.1 - - + +
44B PRO* 3.4 4.7 - - - +
45B ASP* 2.9 54.1 + - + +
77B HIS* 4.0 10.5 - - + +
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Residues in contact with TRP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 3.5 1.0 - - - -
18B TYR* 2.8 60.2 + + + +
25B VAL* 1.3 75.0 - - - +
27B TYR* 1.3 76.8 + - - +
28B GLN* 4.6 3.6 - - + +
42B GLU* 4.0 22.8 - - + +
43B GLY* 3.6 15.5 - - - -
44B PRO* 3.5 39.7 - - + -
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.7 19.1 - - + -
16B ILE 3.4 2.7 - - - +
17B SER* 3.2 29.8 - - - -
25B VAL* 3.4 36.3 - - + +
26B TRP* 1.3 83.0 + - - +
28B GLN* 1.3 60.7 + - - +
41B LEU* 3.6 18.8 - - + -
42B GLU* 3.3 4.9 - - - +
43B GLY 2.7 39.3 + - - +
45B ASP* 4.2 10.3 - - + +
48B THR* 3.7 28.7 - - + -
73B LEU* 3.3 43.7 + - + -
76B PHE* 3.8 6.2 - + - -
77B HIS* 3.8 9.2 - - - +
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Residues in contact with GLN 28 (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* 4.8 0.4 - - - -
16B ILE* 2.7 61.3 + - + +
18B TYR* 3.1 36.3 + - + -
26B TRP* 4.9 4.3 - - + +
27B TYR* 1.3 75.3 - - - +
29B GLY* 1.3 57.6 + - - +
30B ASN* 5.1 4.4 + - - +
41B LEU* 3.4 7.0 - - - +
42B GLU* 4.6 13.7 - - - +
600B NAG 3.5 23.0 + - - -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU 3.0 14.4 - - - -
15B GLN* 4.2 2.9 - - - -
28B GLN* 1.3 78.4 - - - +
30B ASN* 1.3 73.5 + - - +
40B VAL* 3.6 4.9 - - - +
41B LEU* 2.8 40.6 + - - +
607B PTY 4.0 4.0 - - - -
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Residues in contact with ASN 30 (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* 3.5 1.7 - - - -
14B LEU* 2.9 35.4 + - - +
16B ILE* 5.5 1.0 - - - +
28B GLN* 5.0 6.2 + - - +
29B GLY* 1.3 81.7 + - - +
31B ALA* 1.3 60.7 + - - +
37B LEU* 3.6 16.7 - - + +
39B HIS 3.1 15.3 - - - +
40B VAL* 4.6 4.5 - - + -
600B NAG 1.4 72.6 + - - +
607B PTY 3.6 10.5 - - - +
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Residues in contact with ALA 31 (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* 4.1 9.2 - - + -
12B HIS 3.1 13.0 - - - +
13B MET* 3.7 17.9 - - + -
30B ASN* 1.3 74.2 - - - +
32B SER* 1.4 65.5 + - - +
37B LEU* 3.6 3.3 - - - +
38B THR* 3.0 23.0 + - - -
39B HIS* 3.0 30.3 + - + +
600B NAG 3.6 1.3 - - - -
607B PTY 3.8 11.8 - - + +
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 4.0 1.9 - - - +
11B LEU* 3.4 6.4 - - - +
12B HIS* 2.9 34.1 + - - +
31B ALA* 1.4 69.8 - - - +
33B LEU* 1.3 60.2 + - - +
34B GLY 4.2 0.2 + - - -
35B GLY* 4.2 10.8 + - - -
36B HIS 3.0 19.1 - - - -
37B LEU* 3.3 18.0 + - - +
600B NAG 2.7 30.1 + - - -
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Residues in contact with LEU 33 (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 3.4 14.1 - - - +
11B LEU* 4.2 7.4 - - + -
32B SER* 1.3 71.8 - - - +
34B GLY* 1.3 68.3 + - - +
35B GLY 3.1 0.9 - - - -
36B HIS 2.9 17.4 + - - +
38B THR* 3.8 14.3 + - + +
56B LEU* 4.3 8.1 - - + -
172B TYR* 4.0 18.2 - - + -
173B VAL* 4.0 21.5 - - + -
176B HIS* 3.7 35.7 - - + +
177B ILE* 3.7 19.5 - - + -
180B GLU* 3.6 34.5 - - + +
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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