Contacts of the strand formed by residues 101 - 105 (chain A) in PDB entry 2Q7V
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 PHE 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 4.2 10.5 - - + -
91A GLN 3.3 6.1 - - - +
92A HIS* 3.5 31.6 - - + -
99A TYR 3.2 4.7 - - - +
100A PRO* 1.3 87.5 - - + +
102A THR* 1.3 65.2 + - - +
103A VAL* 4.1 0.4 - - + -
111A ARG* 3.4 7.3 - - - +
112A ALA* 3.1 37.8 + - + +
113A LYS 3.6 19.7 - - - -
114A ALA* 4.0 0.2 - - - -
115A VAL* 3.5 31.4 - - + -
276A ILE* 3.9 4.3 - - + -
277A PRO 3.5 20.4 - - - -
278A MET* 3.6 28.3 - - + -
279A LEU* 3.7 22.4 - - + -
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Residues in contact with THR 102 (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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90A VAL* 3.4 1.4 - - - -
91A GLN* 2.6 74.9 + - - +
99A TYR 5.3 1.4 + - - -
100A PRO 5.2 0.9 + - - -
101A PHE* 1.3 75.9 + - - +
103A VAL* 1.3 61.5 + - - +
104A ARG* 4.5 2.5 - - + -
109A GLU* 4.2 27.4 - - + +
110A TYR 3.7 7.9 - - - +
111A ARG* 4.7 14.9 - - + +
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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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12A VAL* 3.9 20.2 - - + -
14A ILE* 4.0 9.0 - - + -
37A LEU* 4.1 12.3 - - + -
87A VAL* 3.8 37.9 - - + -
89A GLY 3.7 3.1 - - - +
90A VAL* 4.5 7.9 - - + +
102A THR* 1.3 75.1 - - - +
104A ARG* 1.3 63.0 + - - +
109A GLU* 3.4 4.0 - - - +
110A TYR* 2.7 55.7 + - + +
112A ALA* 4.9 2.2 - - + -
115A VAL* 4.1 22.2 - - + -
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Residues in contact with ARG 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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87A VAL* 3.5 5.3 - - - -
88A GLN* 2.7 62.2 + - + +
89A GLY* 2.8 22.8 + - - +
91A GLN* 3.1 33.8 + - - +
102A THR* 4.5 1.6 - - + -
103A VAL* 1.3 76.2 - - - +
105A GLY* 1.3 55.4 + - - +
108A GLY 4.1 3.1 - - - +
109A GLU* 3.7 26.6 - - + +
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Residues in contact with GLY 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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85A ASP* 3.3 16.2 - - - -
86A GLU 3.4 11.0 - - - -
87A VAL* 4.1 3.6 - - - -
88A GLN* 3.2 17.4 + - - -
103A VAL 3.8 1.4 + - - -
104A ARG* 1.3 77.0 + - - +
106A TYR* 1.3 64.7 + - - -
107A ASN 3.3 1.1 - - - -
108A GLY 2.9 16.8 + - - +
110A TYR* 4.0 5.9 - - - -
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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