Contacts of the strand formed by residues 34 - 41 (chain A) in PDB entry 3A98
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 VAL 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A HIS* 5.3 0.7 - - + -
13A GLY 3.4 11.2 - - - +
14A VAL* 4.5 4.7 - - + -
32A GLY 3.8 5.6 - - - +
33A ASP* 1.3 75.1 - - - +
35A VAL* 1.3 69.0 + - - +
49A LEU* 3.7 4.4 - - - +
50A ILE* 3.0 44.5 + - + +
51A LYS* 4.8 10.3 + - + +
67A LYS* 5.6 3.4 - - + -
69A VAL* 4.9 17.9 - - + -
700B ASP* 3.4 40.2 - - + +
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Residues in contact with VAL 35 (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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12A HIS* 3.3 8.7 - - - +
13A GLY* 2.8 49.8 + - - +
27A LEU* 5.0 0.2 - - + -
29A LEU* 3.8 29.4 - - + -
33A ASP 4.6 3.6 - - - +
34A VAL* 1.3 81.5 - - - +
36A ARG* 1.3 59.1 + - - +
37A ILE* 4.2 6.5 - - + -
48A TYR 3.3 15.0 - - - +
49A LEU* 3.9 8.5 - - + -
50A ILE* 4.0 5.4 - - - -
59A PHE* 3.8 33.7 - - + -
64A ILE* 4.0 9.4 - - + -
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Residues in contact with ARG 36 (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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7A ALA 5.8 0.6 + - - -
11A ARG* 3.5 37.4 + - - +
12A HIS* 3.3 28.8 + - - -
35A VAL* 1.3 73.8 - - - +
37A ILE* 1.3 88.0 + - - +
38A GLN* 3.8 12.2 + - + +
47A GLY* 3.1 6.1 - - - -
48A TYR* 2.9 64.5 + - + +
50A ILE* 3.5 14.2 - - + +
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Residues in contact with ILE 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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7A ALA* 3.7 16.3 - - + +
10A GLU 3.2 24.7 - - - +
11A ARG* 2.7 11.3 + - - +
12A HIS 4.2 1.6 - - - -
13A GLY* 4.1 16.4 - - - +
35A VAL* 4.2 11.9 - - + -
36A ARG* 1.3 95.1 + - - +
38A GLN* 1.3 61.2 + - - +
39A GLU 3.7 7.0 - - - +
45A TYR* 3.6 43.7 - - + -
46A ARG 3.8 4.5 - - - +
47A GLY* 4.4 0.2 - - - -
59A PHE* 4.3 5.2 - - + -
64A ILE* 4.3 5.8 - - + -
66A ILE* 3.6 30.3 - - + -
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Residues in contact with GLN 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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6A LYS* 3.8 6.4 - - - +
7A ALA* 3.1 19.1 + - - +
36A ARG* 4.3 13.0 - - + +
37A ILE* 1.3 78.7 - - - +
39A GLU* 1.3 71.2 + - + +
46A ARG* 2.8 9.4 + - - +
47A GLY* 3.6 14.6 + - - -
48A TYR* 3.6 27.4 - - + -
56A GLN* 2.7 33.0 + - - +
724B TYR* 3.9 25.1 - - + +
725B ASP 4.7 6.6 + - - -
727B ASN* 4.8 5.1 + - - -
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Residues in contact with GLU 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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4A TRP* 3.5 20.5 - - + +
5A ARG 3.0 17.7 - - - +
6A LYS* 4.4 0.9 - - - -
7A ALA* 3.8 6.7 - - - +
37A ILE* 3.7 5.0 - - - +
38A GLN* 1.3 85.2 - - + +
40A THR* 1.3 62.4 + - - +
45A TYR* 3.3 4.3 - - - -
46A ARG* 2.8 66.6 + - + +
722B PHE* 3.6 2.3 - - - +
723B VAL* 2.9 26.7 + - - +
724B TYR* 3.0 30.5 + - + +
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Residues in contact with THR 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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4A TRP* 3.4 4.9 - - - -
5A ARG* 2.8 71.1 + - + +
6A LYS 4.7 3.1 - - - +
7A ALA* 4.8 1.6 - - - -
10A GLU* 4.2 13.4 + - - +
39A GLU* 1.3 76.8 - - - +
41A CYS* 1.3 63.1 + - - +
42A GLY 4.1 10.7 + - - +
44A TRP 2.7 21.0 + - - -
45A TYR* 3.7 19.6 - - - -
61A LYS* 5.6 2.1 - - - +
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Residues in contact with CYS 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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2A ALA* 2.9 38.4 - - - -
3A PRO 3.5 11.0 - - - +
4A TRP* 3.1 46.4 - - + -
5A ARG* 5.8 1.3 - - - +
40A THR* 1.3 76.2 + - - +
42A GLY* 1.3 63.7 + - - +
43A ASP 3.4 2.8 + - - -
44A TRP* 3.0 22.1 + - - +
717B PRO* 4.7 11.3 - - - +
718B SER* 5.5 1.6 - - - -
719B ASN* 4.5 1.6 - - - -
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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