Contacts of the strand formed by residues 102 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A THR* 3.3 24.0 - - + +
59A VAL 3.5 4.7 + - - -
60A ILE* 3.4 24.0 - - + -
90A HIS* 3.1 40.1 + - + +
100A ASN 3.3 4.0 + - - +
101A GLN* 1.3 81.6 - - - +
103A VAL* 1.3 59.2 + - - +
104A PHE 4.1 1.6 + - - -
105A GLU* 4.4 1.4 + - - +
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Residues in contact with VAL 103 (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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59A VAL* 2.9 31.8 + - + +
60A ILE* 4.4 3.6 - - - +
61A THR* 4.6 6.1 - - + +
67A PHE* 3.8 15.0 - - + -
89A TRP* 4.0 0.7 - - - -
90A HIS* 3.0 22.1 + - - +
91A VAL* 3.5 32.3 - - + +
97A ILE* 3.8 29.6 - - + -
101A GLN* 3.5 4.0 + - - +
102A THR* 1.3 74.6 - - - +
104A PHE* 1.3 80.2 + - + +
291A LEU* 5.0 6.3 - - + -
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Residues in contact with PHE 104 (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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58A THR* 3.8 1.1 - - - +
59A VAL* 3.0 54.0 + - + +
67A PHE* 4.5 8.7 - + - -
73A VAL* 4.3 24.0 - - + -
77A PHE* 5.9 0.2 - + - -
87A LEU* 4.3 7.0 - - + -
88A THR 3.1 16.4 - - - +
89A TRP* 3.5 36.8 - + + +
90A HIS* 4.3 2.7 - - - +
102A THR* 3.7 1.8 + - - -
103A VAL* 1.3 95.1 - - + +
105A GLU* 1.3 76.8 + - - +
106A LEU* 3.7 30.1 - - + -
120A ALA* 5.8 6.5 - - + -
121A LEU* 5.9 2.9 - - + -
124A VAL* 5.4 4.9 - - + -
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Residues in contact with GLU 105 (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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56A HIS* 3.2 30.1 + - + +
57A ALA 3.6 8.7 - - - +
58A THR* 3.4 21.6 + - + +
87A LEU* 3.6 8.5 - - - +
88A THR* 2.8 43.6 + - - +
90A HIS* 3.1 31.2 + - + +
102A THR* 4.6 0.9 + - - +
104A PHE* 1.3 79.5 - - - +
106A LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 106 (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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56A HIS* 3.2 32.0 - - - -
57A ALA* 2.9 23.0 + - + +
59A VAL* 3.8 17.9 - - + -
77A PHE* 3.5 41.1 - - + -
85A VAL* 5.0 1.1 - - + -
86A ARG 3.7 2.9 - - - -
87A LEU* 3.7 18.2 - - + -
104A PHE* 3.7 22.7 - - + -
105A GLU* 1.3 78.4 - - - +
107A GLN* 1.3 62.8 + - - +
113A LEU* 4.2 16.8 - - + -
120A ALA* 5.9 0.4 - - + -
293A MET* 3.9 20.0 - - - -
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Residues in contact with GLN 107 (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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54A GLN* 5.6 0.9 - - - +
55A ALA 3.9 2.1 - - - +
56A HIS* 3.0 41.6 - - + +
84A ASP 3.9 0.3 - - - +
85A VAL* 3.1 9.2 - - - +
86A ARG* 2.8 65.2 + - + +
88A THR* 5.0 10.5 - - + +
106A LEU* 1.3 77.0 - - - +
108A GLY* 1.3 58.7 + - - +
113A LEU* 4.5 0.4 - - - -
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Residues in contact with GLY 108 (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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54A GLN* 3.7 15.8 + - - -
55A ALA 2.8 33.4 + - - +
84A ASP 3.7 4.9 - - - -
85A VAL* 4.3 5.6 - - - -
107A GLN* 1.3 75.1 - - - +
109A PRO* 1.3 76.9 - - - +
110A ALA 3.4 0.2 + - - -
113A LEU* 3.4 6.9 - - - +
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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