Contacts of the strand formed by residues 18 - 24 (chain A) in PDB entry 1T7K
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 GLN 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE 3.6 0.7 - - - +
14A LYS* 3.3 5.0 - - - -
15A ILE* 2.7 42.3 + - - +
16A GLY 3.6 12.4 + - - +
17A GLY* 1.3 75.7 - - - +
19A LEU* 1.3 63.8 + - - +
20A LYS* 2.9 30.7 + - + +
36A MET* 3.5 28.4 - - - +
37A SER* 4.5 9.3 + - - +
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Residues in contact with LEU 19 (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 THR* 4.1 20.6 - - + -
13A ILE 3.4 13.5 - - - +
14A LYS* 3.9 28.5 - - + -
17A GLY 4.4 0.8 + - - +
18A GLN* 1.3 73.9 - - - +
20A LYS* 1.3 63.4 + - - +
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Residues in contact with LYS 20 (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 THR* 3.3 7.9 - - - -
13A ILE* 2.8 44.3 + - + +
15A ILE* 4.4 10.3 - - + +
18A GLN* 2.9 43.7 + - + +
19A LEU* 1.3 78.8 - - - +
21A GLU* 1.3 62.0 + - - +
33A LEU* 5.0 6.1 - - + -
34A GLU* 5.0 6.7 - - - -
35A GLU 5.4 2.0 - - - -
36A MET* 3.5 33.9 - - - +
83A ASN* 3.9 28.7 - - - +
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Residues in contact with GLU 21 (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 LEU* 3.8 38.0 - - + +
11A VAL 3.3 11.0 - - - +
12A THR* 4.5 3.8 - - - +
20A LYS* 1.3 75.5 - - - +
22A ALA* 1.3 62.7 + - - +
82A VAL* 5.9 0.2 - - - +
83A ASN* 3.0 26.5 + - - +
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Residues in contact with ALA 22 (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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9A PRO 3.7 0.2 - - - +
10A LEU* 3.2 10.7 - - - -
11A VAL* 2.8 39.9 + - + +
13A ILE* 4.3 13.0 - - + -
21A GLU* 1.3 78.0 - - - +
23A LEU* 1.3 63.1 + - - +
82A VAL* 5.6 1.1 - - - -
83A ASN* 3.4 18.2 - - + +
85A ILE* 3.6 31.9 - - + -
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Residues in contact with LEU 23 (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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8A ARG* 3.9 28.3 - - + +
9A PRO* 3.6 34.5 - - + -
10A LEU* 3.6 10.5 - - + -
22A ALA* 1.3 72.6 - - - +
24A LEU* 1.3 61.7 + - - +
25A ASP* 3.1 8.9 + - + +
82A VAL* 4.3 13.2 - - + +
83A ASN 2.9 15.8 + - - +
84A ILE* 3.7 9.6 - - + -
85A ILE* 2.9 26.2 + - - -
26B THR 4.2 0.2 - - - +
27B GLY* 3.5 38.6 - - - +
1000B BH0 4.3 14.4 - - + -
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Residues in contact with LEU 24 (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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3A ILE* 3.8 23.8 - - + -
9A PRO* 3.0 28.9 + - + +
11A VAL* 3.7 41.3 - - + -
22A ALA 3.9 0.2 + - - -
23A LEU* 1.3 68.8 - - - +
25A ASP* 1.3 59.8 + - - +
26A THR 4.1 0.2 - - - -
66A ILE* 4.3 9.0 - - + -
67A CYS* 5.1 0.7 - - - -
85A ILE* 4.0 15.0 - - + -
90A LEU* 3.7 27.8 - - + -
93A ILE* 5.2 1.3 - - + -
95A CYS* 5.4 1.6 - - - -
26B THR* 2.8 19.2 + - - -
97B LEU* 3.9 21.3 - - + -
99B PHE* 4.4 9.6 - - + -
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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