Contacts of the strand formed by residues 57 - 62 (chain A) in PDB entry 2QV8
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 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.7 31.9 - - + -
49A GLU* 3.6 29.4 - - + -
50A ALA* 3.9 15.7 - - + -
53A SER* 3.9 5.6 - - - -
55A GLN* 3.5 36.1 - - + -
56A ASP* 1.3 75.0 - - - +
58A GLY* 1.3 59.9 + - - +
71A LEU 3.2 20.4 - - - +
72A GLN* 3.6 25.6 - - + -
79A TRP* 3.4 16.7 - - - -
82A TRP* 3.7 27.8 - + - -
142A PHE* 3.7 1.6 - - - +
143A VAL* 2.8 33.8 + - + +
144A LEU* 5.2 0.3 - - - +
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Residues in contact with GLY 58 (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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46A LEU* 3.7 5.1 - - - +
57A PHE* 1.3 79.2 - - - +
59A VAL* 1.3 64.3 + - - -
60A ARG 4.2 0.2 - - - -
70A PHE* 3.6 3.8 - - - -
71A LEU* 2.8 33.0 + - - +
79A TRP* 3.6 1.4 - - - -
139A PRO* 3.9 16.2 - - - -
141A LEU 3.0 12.6 - - - -
143A VAL* 4.2 4.9 - - - -
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Residues in contact with VAL 59 (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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39A PHE* 4.0 25.6 - - + -
43A LEU* 4.5 13.9 - - + -
46A LEU* 3.8 18.8 - - + -
58A GLY* 1.3 77.7 - - - +
60A ARG* 1.3 69.1 + - - +
61A ILE* 4.0 11.7 - - + -
68A LEU* 4.4 5.4 - - + -
69A THR 3.3 11.0 - - - +
70A PHE* 3.9 17.0 - - + -
139A PRO* 3.2 7.6 - - - +
140A GLN* 3.2 3.6 + - - +
141A LEU* 2.9 44.7 + - + +
143A VAL* 4.6 2.9 - - + -
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Residues in contact with ARG 60 (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* 1.3 74.7 - - - +
61A ILE* 1.3 62.9 + - - +
62A ASP* 3.1 37.9 + - - +
67A ARG 3.8 0.9 - - - +
68A LEU* 3.4 5.0 - - - -
69A THR* 2.9 49.6 + - - +
71A LEU* 4.0 11.7 - - + +
90A GLN* 4.5 4.9 - - - +
136A GLU* 2.9 31.3 + - - +
137A PRO* 3.0 52.4 + - - +
138A ALA 3.6 12.1 - - - +
139A PRO* 3.9 8.6 - - + +
140A GLN* 3.3 14.8 - - - +
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Residues in contact with ILE 61 (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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39A PHE* 6.0 1.1 - - + -
59A VAL* 4.4 7.6 - - + -
60A ARG* 1.3 74.9 - - - +
62A ASP* 1.3 66.8 + - - +
63A VAL* 3.8 3.3 + - + -
67A ARG 3.7 2.9 - - - -
68A LEU* 3.9 17.7 - - + -
99A LEU* 3.7 25.8 - - + -
101A PHE* 3.5 57.2 - - + -
140A GLN* 2.9 35.0 + - - +
141A LEU* 3.9 28.9 - - + -
152A PHE* 5.1 2.7 - - + -
154A LEU* 4.0 13.2 - - + -
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Residues in contact with ASP 62 (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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60A ARG* 3.1 45.6 + - - +
61A ILE* 1.3 78.5 - - - +
63A VAL* 1.3 59.6 + - - +
64A ASP 3.2 2.2 - - - +
65A THR* 3.3 20.6 + - + +
66A ARG* 2.9 24.9 + - - -
67A ARG* 2.9 27.5 + - + +
69A THR* 4.4 5.0 + - - -
99A LEU* 4.1 2.0 - - - +
140A GLN* 5.1 0.7 + - - -
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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