Contacts of the strand formed by residues 102 - 109 (chain B) in PDB entry 1QAP
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 THR 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B THR* 3.3 29.9 - - - +
59B VAL 3.7 5.7 + - - -
60B ILE* 4.6 4.0 - - - +
90B HIS* 3.3 40.8 + - + +
91B VAL* 5.0 0.5 - - - +
100B ASN 3.7 2.4 + - - -
101B GLN* 1.3 85.6 - - + +
103B VAL* 1.3 61.2 + - - +
104B PHE 4.2 3.5 + - - -
105B GLU* 5.0 0.2 - - - +
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Residues in contact with VAL 103 (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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59B VAL* 3.2 14.2 + - + +
60B ILE* 4.3 1.8 - - - -
61B THR* 3.2 37.9 - - + +
67B PHE* 3.6 29.6 - - + -
89B TRP* 4.7 1.0 - - + -
90B HIS* 3.1 28.8 + - - +
91B VAL* 3.2 28.2 + - + +
97B ILE* 4.5 7.0 - - + -
101B GLN* 4.1 4.5 - - - +
102B THR* 1.3 73.1 - - - +
104B PHE* 1.3 78.7 + - + +
291B LEU* 4.7 2.0 - - + -
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Residues in contact with PHE 104 (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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58B THR* 3.7 2.8 - - - +
59B VAL* 3.0 68.7 + - + +
67B PHE* 5.2 0.9 - + - -
73B VAL* 3.5 37.7 - - + -
77B PHE* 6.0 0.2 - + - -
87B LEU* 4.8 1.1 - - + -
88B THR 2.9 19.5 - - - +
89B TRP* 3.6 34.8 - + + -
90B HIS* 5.1 1.6 - - - -
102B THR* 3.8 4.4 + - - -
103B VAL* 1.3 94.7 - - + +
105B GLU* 1.3 61.8 + - - +
106B LEU* 3.8 27.8 - - + -
120B ALA* 5.8 2.9 - - + -
121B LEU* 5.2 5.6 - - + -
124B VAL* 5.2 8.5 - - + -
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Residues in contact with GLU 105 (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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56B HIS* 3.0 34.8 + - - +
57B ALA 3.4 4.3 - - - +
58B THR* 3.7 23.2 - - + +
86B ARG 4.3 0.4 - - - -
87B LEU* 3.2 1.0 - - - +
88B THR* 2.9 54.3 + - + +
90B HIS* 5.0 8.7 + - - +
102B THR* 5.0 2.2 - - - +
104B PHE* 1.3 73.1 - - - +
106B LEU* 1.3 76.2 + - - +
107B GLN* 3.9 6.6 - - + +
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Residues in contact with LEU 106 (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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55B ALA 3.5 1.3 - - - +
56B HIS* 3.2 2.9 - - - -
57B ALA* 2.8 39.9 + - + +
59B VAL* 4.8 4.5 - - + -
77B PHE* 3.8 23.1 - - + -
85B VAL* 4.9 1.3 - - + -
86B ARG 3.3 2.7 - - - +
87B LEU* 3.3 31.9 - - + -
104B PHE* 3.8 21.5 - - + -
105B GLU* 1.3 88.3 - - - +
107B GLN* 1.3 73.4 + - - +
108B GLY 4.1 0.4 - - - -
113B LEU* 4.1 17.8 - - + +
293B MET* 3.8 33.0 - - + -
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Residues in contact with GLN 107 (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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55B ALA 3.7 4.6 + - - -
56B HIS* 2.8 45.0 - - - +
84B ASP 4.4 0.3 - - - +
85B VAL* 3.5 3.9 - - - -
86B ARG* 2.7 60.5 + - + +
88B THR* 5.2 3.6 - - - +
105B GLU* 3.9 6.3 - - - +
106B LEU* 1.3 84.9 - - - +
108B GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 108 (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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54B GLN* 4.0 15.1 + - - +
55B ALA 2.8 35.4 + - - +
84B ASP 4.1 4.5 - - - -
85B VAL* 4.6 0.9 - - - -
107B GLN* 1.3 75.2 - - - +
109B PRO* 1.3 73.1 - - - +
110B ALA 3.5 0.2 + - - -
113B LEU* 3.7 13.8 - - - +
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Residues in contact with PRO 109 (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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52B ASP* 5.3 8.7 - - - +
53B THR 4.1 1.8 - - - +
54B GLN* 4.1 16.5 - - + +
81B ALA* 5.6 0.2 - - + -
84B ASP* 3.4 25.4 - - + +
85B VAL* 4.4 5.8 - - + -
108B GLY* 1.3 80.7 - - - +
110B ALA* 1.3 66.5 + - - +
111B ARG* 3.3 4.5 - - + +
112B VAL* 3.1 34.6 + - + +
113B LEU* 3.1 13.2 + - - +
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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