Contacts of the strand formed by residues 36 - 44 (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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A SER* 3.2 3.8 - - - -
33A LEU* 2.9 40.9 + - + +
34A GLY 3.3 0.4 - - - -
35A GLY* 1.3 76.6 - - - +
37A LEU* 1.3 81.8 + - - +
38A THR* 3.4 14.1 + - + +
54A GLN* 2.4 33.1 + - - -
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Residues in contact with LEU 37 (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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30A ASN* 3.9 18.8 - - + +
31A ALA 3.5 16.4 - - - +
32A SER* 3.5 12.9 + - - +
35A GLY 3.9 3.2 + - - -
36A HIS* 1.3 90.7 + - + +
38A THR* 1.3 59.0 + - - +
39A HIS 3.8 11.4 - - - +
40A VAL* 4.4 6.5 - - + -
53A LEU* 3.6 30.4 - - + +
54A GLN* 4.6 1.0 - - - +
603A NAG 4.2 23.1 - - + -
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Residues in contact with THR 38 (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* 4.6 1.0 - - - +
31A ALA* 2.9 17.1 + - - +
32A SER* 3.7 4.2 + - - -
33A LEU* 3.9 29.7 + - + +
36A HIS* 3.4 28.3 - - + +
37A LEU* 1.3 74.8 - - - +
39A HIS* 1.3 91.5 + - - +
52A GLN* 3.5 2.4 - - - +
53A LEU* 2.9 30.5 + - - +
54A GLN* 4.3 4.3 + - - +
56A LEU* 4.0 14.4 - - + +
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Residues in contact with HIS 39 (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* 5.3 1.1 - - + -
30A ASN* 3.1 9.4 - - - +
31A ALA* 3.0 33.8 + - + +
37A LEU* 3.8 1.6 - - - +
38A THR* 1.3 108.2 + - - +
40A VAL* 1.3 66.7 + - - +
51A ILE 3.2 7.4 - - - +
52A GLN* 3.6 28.7 + - + +
53A LEU* 4.3 3.0 - - - +
56A LEU* 4.4 1.6 - - + -
57A GLN* 4.9 0.2 + - - -
62A TRP* 3.7 23.7 - + - -
172A TYR* 3.1 34.9 + + - -
606A PTY 3.6 38.2 - - + +
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Residues in contact with VAL 40 (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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29A GLY 3.6 7.4 - - - +
30A ASN* 4.1 10.1 - - + +
37A LEU* 4.4 9.4 - - + -
39A HIS* 1.3 82.1 - - - +
41A LEU* 1.3 63.3 + - - +
42A GLU* 6.2 0.9 - - + -
49A THR* 4.1 1.5 - - + +
50A ILE* 3.6 4.0 - - - +
51A ILE* 2.9 59.2 + - + +
53A LEU* 4.1 22.4 - - + +
603A NAG 5.4 6.3 - - - +
606A PTY 5.0 0.4 - - - -
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Residues in contact with LEU 41 (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* 5.4 3.8 - - + -
27A TYR* 3.7 30.1 - - + -
28A GLN* 3.4 2.0 - - - +
29A GLY* 2.8 44.8 + - - +
40A VAL* 1.3 77.7 - - - +
42A GLU* 1.3 66.7 + - - +
48A THR* 3.7 15.0 - - + -
49A THR 3.2 6.3 - - - -
50A ILE* 4.1 20.6 - - + -
69A LEU* 5.3 3.4 - - + -
73A LEU* 4.3 16.6 - - + -
606A PTY 3.9 44.6 - - + -
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Residues in contact with GLU 42 (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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26A TRP* 2.8 36.1 + - + +
27A TYR 3.2 6.5 - - - +
28A GLN* 3.0 35.5 + - - +
40A VAL* 6.2 1.3 - - + -
41A LEU* 1.3 78.1 - - - +
43A GLY* 1.3 62.9 + - - +
47A ASN 4.2 0.2 - - - +
48A THR* 4.1 2.7 - - - -
49A THR* 2.8 36.6 + - - +
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Residues in contact with GLY 43 (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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26A TRP* 3.8 16.1 - - - -
27A TYR* 2.9 34.6 + - - +
42A GLU* 1.3 80.1 - - - +
44A PRO* 1.3 76.0 - - - +
47A ASN 3.7 6.3 - - - -
48A THR* 3.8 3.4 + - - +
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Residues in contact with PRO 44 (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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25A VAL 3.5 9.6 - - - +
26A TRP* 3.6 26.9 - - + -
27A TYR* 4.7 0.2 - - - -
43A GLY* 1.3 85.9 - - - +
45A ASP* 1.3 62.8 + - - +
46A THR* 3.0 20.2 - - + +
47A ASN* 2.9 32.0 + - + +
48A THR* 2.7 21.8 + - - -
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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