Contacts of the strand formed by residues 95 - 99 (chain A) in PDB entry 2Q41
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 VAL 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.2 17.9 - - - +
51A MSE 5.9 0.7 - - - +
52A SER* 5.0 5.8 - - - -
55A TRP* 3.4 34.1 - - + -
91A VAL* 3.8 0.7 - - - -
92A LEU 3.1 24.6 + - - +
93A ASP* 4.7 5.4 - - + +
94A GLY* 1.3 75.6 - - - +
96A ILE* 1.3 75.5 + - - +
97A GLN* 2.8 14.9 + - - +
204A ASP* 3.8 19.5 - - - +
270A TYR* 5.7 2.2 - - + -
271A PRO* 5.4 4.7 - - + -
72C LYS* 6.0 0.9 - - - +
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Residues in contact with ILE 96 (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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48A PHE* 3.6 31.6 - - + -
50A GLU* 2.6 39.7 + - + +
60A HIS* 4.9 8.7 - - + +
62A LEU* 4.0 21.3 - - + -
89A VAL* 4.1 7.0 - - + -
90A LEU 3.9 3.8 - - - -
91A VAL* 4.2 3.6 - - - -
94A GLY 3.5 1.2 + - - -
95A VAL* 1.3 78.2 - - - +
97A GLN* 1.3 61.6 + - - +
98A LEU* 3.7 22.2 - - - +
99A THR* 4.1 11.9 - - - +
269A THR* 3.7 23.3 - - - +
270A TYR* 3.7 15.7 - - + -
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Residues in contact with GLN 97 (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 LEU* 2.8 27.5 + - + +
92A LEU* 3.5 45.6 + - + +
95A VAL* 2.8 19.8 + - - +
96A ILE* 1.3 75.2 + - - +
98A LEU* 1.3 69.5 + - + +
106A TYR* 5.6 1.2 - - - -
128A GLY 5.7 0.7 - - - +
130A GLY* 5.3 7.0 - - - +
201A ASP* 4.6 6.2 - - - +
202A SER 4.6 4.0 - - - +
203A SER* 3.2 28.6 + - - +
234A GLN* 5.6 0.7 + - - -
270A TYR* 3.3 18.4 + - - -
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Residues in contact with LEU 98 (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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89A VAL* 3.6 3.8 - - - +
90A LEU* 3.3 52.9 + - + +
96A ILE* 3.3 7.8 - - - +
97A GLN* 1.3 83.4 - - + +
99A THR* 1.3 81.2 + - - +
100A GLU* 4.5 0.4 - - - +
102A ASP* 5.6 0.2 - - - -
103A GLU* 4.7 16.4 - - + +
106A TYR* 6.3 0.9 - - + -
107A GLN* 5.3 0.9 - - - +
130A GLY 4.4 1.6 - - - +
131A ASP* 3.4 40.6 - - + +
164A PHE* 4.3 20.4 - - + -
167A VAL* 5.7 0.9 - - + -
269A THR* 5.0 1.6 - - - -
270A TYR* 4.7 9.0 - - - +
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Residues in contact with THR 99 (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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62A LEU* 4.6 1.7 - - - +
86A TYR* 3.4 36.5 - - + +
88A LYS 3.9 5.2 - - - -
89A VAL* 3.9 17.2 - - - +
96A ILE* 4.1 1.9 - - - +
98A LEU* 1.3 83.7 + - - +
100A GLU* 1.3 61.6 + - - +
101A ARG 3.2 14.6 - - - +
102A ASP* 3.6 18.4 + - - +
103A GLU* 2.8 31.6 + - - +
269A THR* 3.6 19.4 + - - +
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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