Contacts of the strand formed by residues 152 - 158 (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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.8 11.2 - + - -
43A LEU* 3.7 26.9 - - + -
61A ILE* 5.1 3.1 - - + -
101A PHE* 5.3 0.9 - - + -
102A GLU 3.3 14.6 - - - +
103A LEU* 4.1 2.2 - - + -
104A GLY* 4.1 5.4 - - - +
141A LEU* 3.5 44.2 - - + -
149A VAL* 4.3 4.9 - - + -
150A THR 3.2 19.9 + - - -
151A PRO* 1.3 75.9 - - - +
153A THR* 1.3 72.6 + - - +
154A LEU* 3.6 15.3 - - + -
169A VAL* 3.4 22.0 - - + -
170A THR* 3.1 10.6 - - - +
171A ALA* 3.0 51.1 + - + -
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Residues in contact with THR 153 (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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101A PHE* 3.1 6.9 - - - +
102A GLU* 2.9 54.4 + - - +
104A GLY 5.5 1.4 + - - -
108A TRP* 4.1 12.6 - - + -
152A PHE* 1.3 78.1 + - - +
154A LEU* 1.3 60.0 + - - +
168A ARG* 3.7 33.2 - - + -
169A VAL 3.5 4.5 - - - -
170A THR* 3.2 23.5 + - - +
180A LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 154 (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* 3.6 32.5 - - + -
61A ILE* 4.0 28.7 - - + -
68A LEU* 4.2 15.5 - - + -
99A LEU* 4.1 15.5 - - + -
100A ASP 3.3 17.3 - - - +
101A PHE* 4.2 3.8 - - + -
152A PHE* 3.6 17.8 - - + -
153A THR* 1.3 75.0 - - - +
155A SER* 1.3 61.9 + - - +
156A ILE* 3.9 24.9 + - + +
168A ARG* 3.1 6.6 - - - +
169A VAL* 2.8 34.2 + - + +
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Residues in contact with SER 155 (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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99A LEU* 3.1 9.5 - - - +
100A ASP 2.8 30.2 + - - -
108A TRP* 3.7 22.4 - - - -
154A LEU* 1.3 75.1 - - - +
156A ILE* 1.3 63.5 + - - +
157A PHE* 3.3 7.8 - - - -
163A PRO* 2.7 34.1 + - - -
166A GLN* 3.3 12.1 - - - +
167A TRP 3.4 4.3 - - - -
168A ARG* 4.0 6.5 - - - -
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Residues in contact with ILE 156 (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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32A ALA* 3.9 13.4 - - - +
35A SER* 3.8 26.7 - - - +
36A ALA* 3.7 32.1 - - + +
39A PHE* 4.8 3.1 - - + -
68A LEU* 5.2 3.4 - - + -
93A LEU* 4.1 18.2 - - + -
97A LEU* 4.2 11.7 - - + -
98A GLN 3.5 10.3 - - - +
99A LEU* 4.3 7.4 - - + -
154A LEU* 3.9 26.2 - - + +
155A SER* 1.3 77.1 - - - +
157A PHE* 1.3 68.2 + - - +
166A GLN* 3.7 0.7 - - - +
167A TRP* 2.9 33.5 + - - +
169A VAL* 5.8 0.9 - - + -
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Residues in contact with PHE 157 (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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32A ALA* 4.5 3.1 - - - -
97A LEU* 3.3 8.5 - - - -
98A GLN* 2.7 60.4 + - + +
99A LEU* 3.8 9.9 - - - -
100A ASP* 3.8 11.0 - - + -
110A LYS* 5.8 3.6 - - + -
155A SER* 3.3 30.5 - - - -
156A ILE* 1.3 78.6 - - - +
158A PRO* 1.3 80.5 - - + +
161A GLN 3.2 24.5 - - - -
162A GLU 4.0 4.9 - - - -
163A PRO* 3.6 30.3 - - + -
166A GLN* 3.4 27.8 - - + +
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Residues in contact with PRO 158 (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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32A ALA* 4.9 7.0 - - + -
96A GLY 3.4 9.9 - - - +
97A LEU* 4.2 9.6 - - + -
157A PHE* 1.3 96.9 - - + +
159A LYS* 1.3 69.7 + - - +
161A GLN* 3.3 46.9 + - - +
166A GLN* 4.3 5.2 - - - +
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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