Contacts of the strand formed by residues 162 - 166 (chain D) in PDB entry 2Q2U
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 GLY 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D PRO* 3.7 5.4 - - - +
27D LYS* 3.0 23.6 + - - +
152D GLU* 6.0 2.2 - - - -
155D VAL* 3.9 12.1 - - - +
156D LEU* 4.4 10.5 - - - -
160D PHE* 3.2 5.5 - - - +
161D GLU* 1.3 82.0 - - - +
163D VAL* 1.3 61.4 + - - +
187D MET 3.4 13.0 - - - -
188D LYS* 4.7 1.8 - - - -
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Residues in contact with VAL 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ALA* 3.7 14.8 - - + -
25D THR 3.2 14.1 - - - +
27D LYS* 4.0 1.4 - - - +
148D LEU* 4.6 4.3 - - + -
151D TYR* 3.5 29.8 - - + -
152D GLU* 4.7 6.5 - - + -
155D VAL* 4.5 4.5 - - + -
162D GLY* 1.3 75.1 - - - +
164D MET* 1.3 71.2 + - - +
165D ILE* 3.9 4.4 + - + -
185D LEU 3.8 0.5 - - - +
187D MET* 3.0 73.2 + - + +
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Residues in contact with MET 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.7 17.3 - - + -
23D LEU 3.8 0.7 - - - +
24D ALA* 3.2 5.9 - - - -
25D THR* 2.7 45.6 + - - +
26D PRO 4.5 0.9 - - - +
27D LYS* 3.4 44.4 - - + +
163D VAL* 1.3 72.9 - - - +
165D ILE* 1.3 60.9 + - - +
166D ARG* 4.0 7.5 + - + +
184D LEU* 3.7 31.9 - - + -
185D LEU 3.3 0.2 - - - -
186D LYS* 3.8 25.4 - - + -
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.6 30.7 - - + -
18D VAL* 4.0 12.3 - - + -
22D CYS* 3.4 35.0 - - + -
23D LEU 3.7 2.2 - - - -
24D ALA* 4.5 3.8 - - + +
148D LEU* 3.9 23.8 - - + -
163D VAL* 4.5 15.0 - - + +
164D MET* 1.3 74.0 - - - +
166D ARG* 1.3 64.6 + - - +
182D GLY 5.1 0.7 - - - +
184D LEU* 3.4 2.1 + - - -
185D LEU* 2.6 59.1 + - + +
187D MET* 4.0 9.4 - - + -
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Residues in contact with ARG 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.0 10.3 - - - +
22D CYS* 3.4 9.4 - - - +
23D LEU* 2.8 36.3 + - - +
25D THR* 5.7 3.3 + - + +
65D ASP* 5.3 0.4 + - - -
98D PHE* 3.5 37.0 + - - +
99D ASP* 2.7 26.9 + - - -
109D TYR* 3.2 56.5 + - + -
112D ARG* 3.5 6.3 - - - +
164D MET* 4.8 7.8 - - + +
165D ILE* 1.3 78.6 - - - +
167D LYS* 1.3 61.1 + - - +
182D GLY 4.1 1.8 - - - -
183D ILE* 3.1 17.0 - - - +
184D LEU* 3.8 31.0 - - + +
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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