Contacts of the strand formed by residues 36 - 44 (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 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B SER* 3.0 3.4 - - - -
33B LEU 2.9 33.7 + - - +
34B GLY 3.2 2.3 + - - +
35B GLY* 1.3 78.4 - - - +
37B LEU* 1.3 90.8 + - + +
38B THR* 3.1 8.5 + - + +
53B LEU* 5.9 2.0 - - + +
54B GLN* 3.4 30.6 + - - +
180B GLU* 3.6 17.7 - - + +
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Residues in contact with LEU 37 (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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30B ASN* 3.6 27.1 - - + +
31B ALA 3.8 7.2 - - - +
32B SER* 3.3 12.1 + - - +
35B GLY 3.9 2.2 + - - -
36B HIS* 1.3 92.6 + - + +
38B THR* 1.4 55.5 + - - +
39B HIS 3.4 23.8 - - - +
40B VAL* 3.9 9.0 - - + -
53B LEU* 3.6 30.7 - - + +
600B NAG 4.1 10.8 - - - +
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Residues in contact with THR 38 (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* 4.8 0.5 - - - +
31B ALA* 3.0 10.6 + - - +
32B SER 4.2 0.3 - - - -
33B LEU* 3.8 19.3 + - + +
36B HIS* 3.1 26.0 + - + +
37B LEU* 1.4 72.7 - - - +
39B HIS* 1.4 86.9 + - - +
52B GLN* 3.5 1.6 - - - +
53B LEU* 2.7 38.1 + - - -
54B GLN* 4.1 5.6 + - - +
56B LEU* 3.9 21.0 - - + +
180B GLU* 3.9 12.6 - - - +
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Residues in contact with HIS 39 (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* 5.2 1.3 - - + -
30B ASN* 3.1 9.5 - - - +
31B ALA* 3.0 32.1 + - + +
37B LEU* 3.4 3.6 - - - +
38B THR* 1.4 109.2 + - - +
40B VAL* 1.3 67.3 + - - +
51B ILE 3.2 7.6 - - - +
52B GLN* 3.6 20.6 + - + +
53B LEU* 4.6 0.9 - - - +
56B LEU* 4.2 1.8 - - + -
62B TRP* 3.6 33.8 - + - -
172B TYR* 3.2 31.4 + + - -
607B PTY 3.6 42.7 - - + +
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Residues in contact with VAL 40 (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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29B GLY 3.6 9.0 - - - +
30B ASN* 4.7 3.4 - - + -
37B LEU* 3.9 15.5 - - + -
39B HIS* 1.3 80.8 - - - +
41B LEU* 1.3 72.0 + - - +
42B GLU* 4.4 9.9 - - + +
49B THR 3.8 1.0 - - - +
50B ILE* 3.4 2.6 - - - +
51B ILE* 2.9 48.2 + - + +
53B LEU* 4.1 16.4 - - + -
607B PTY 5.1 1.1 - - - -
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Residues in contact with LEU 41 (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* 5.5 3.4 - - + -
27B TYR* 3.6 31.0 - - + -
28B GLN* 3.4 2.8 - - - +
29B GLY* 2.8 43.1 + - - +
40B VAL* 1.3 78.2 - - - +
42B GLU* 1.3 65.7 + - - +
48B THR* 3.8 8.3 - - + -
49B THR 3.3 2.9 - - - -
50B ILE* 3.6 35.7 - - + -
69B LEU* 5.3 2.9 - - + -
73B LEU* 4.2 16.2 - - + -
607B PTY 3.9 44.0 - - + -
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Residues in contact with GLU 42 (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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26B TRP* 4.0 22.9 - - + +
27B TYR 3.3 11.9 - - - +
28B GLN* 4.9 12.1 - - + +
40B VAL* 4.4 10.7 - - + +
41B LEU* 1.3 76.9 - - - +
43B GLY* 1.3 60.3 + - - +
47B ASN 4.0 0.7 - - - +
48B THR* 4.1 3.8 - - - -
49B THR* 2.8 44.9 + - - +
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Residues in contact with GLY 43 (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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26B TRP* 3.9 14.8 - - - -
27B TYR* 2.7 44.0 + - - +
42B GLU* 1.3 77.5 - - - +
44B PRO* 1.4 76.0 - - - +
47B ASN 3.8 4.7 - - - -
48B THR* 4.3 1.5 - - - +
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Residues in contact with PRO 44 (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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25B VAL 3.4 10.5 - - - +
26B TRP* 3.5 30.2 - - + -
27B TYR* 4.7 0.4 - - - -
43B GLY* 1.4 85.6 - - - +
45B ASP* 1.3 67.3 + - - +
46B THR* 3.6 21.1 - - + +
47B ASN* 3.0 29.6 + - + +
48B THR* 2.9 17.9 + - - -
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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