Contacts of the strand formed by residues 170 - 176 (chain B) in PDB entry 3CKR
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 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ARG* 3.3 7.9 + - - +
8B GLY* 2.6 58.7 + - - +
9B LYS 4.0 7.4 - - - +
10B SER* 4.3 16.8 - - - +
11B GLY 5.6 1.1 - - - +
13B GLY 4.2 4.3 - - - +
14B TYR* 3.4 32.1 - - + +
155B CYS 3.6 5.6 - - - +
156B GLY* 3.2 26.5 - - - +
157B ALA* 4.9 1.3 - - + -
169B SER* 1.3 76.6 - - - +
171B GLY* 1.3 59.2 + - - +
339B GLU* 4.9 2.2 - - - +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU 3.1 17.0 - - - -
7B ARG* 3.6 13.7 - - - -
14B TYR* 3.0 23.1 - - - -
155B CYS* 3.2 19.9 + - - +
156B GLY 4.2 1.0 + - - -
169B SER 4.1 0.6 + - - -
170B VAL* 1.3 74.5 - - - +
172B GLY* 1.3 58.2 + - - -
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASP* 3.5 14.6 + - - -
5B ASN 3.4 4.0 + - - -
6B LEU* 2.6 38.4 + - - +
153B GLN* 3.4 15.5 - - - -
154B LEU* 4.7 0.9 - - - -
155B CYS* 3.8 12.9 - - - -
171B GLY* 1.3 72.2 - - - -
173B SER* 1.3 56.3 + - - -
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B MET 3.7 6.5 - - - -
3B VAL* 3.8 5.4 - - - +
4B ASP* 3.0 32.3 + - - -
5B ASN* 3.5 7.0 - - - -
6B LEU* 3.7 7.5 - - - +
151B SER 3.9 1.2 - - - +
152B LEU* 3.9 2.4 - - - +
153B GLN* 3.3 45.7 + - - +
172B GLY* 1.3 70.1 - - - -
174B MET* 1.3 60.9 + - - +
175B ILE* 4.1 4.6 + - - +
183B LEU* 4.1 17.2 - - - +
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Residues in contact with MET 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B MET* 3.7 4.0 - - - +
5B ASN* 2.8 39.3 + - - +
6B LEU* 3.7 6.2 - - + +
16B VAL* 4.0 35.4 - - + -
31B VAL* 4.4 11.9 - - + -
87B ILE* 4.4 15.5 - - + -
119B LEU* 5.1 4.9 - - + -
121B LEU* 4.7 16.2 - - - -
150B PHE* 5.1 4.5 - - + -
151B SER 3.7 1.6 - - - +
152B LEU* 3.4 26.7 - - + -
173B SER* 1.3 72.7 - - - +
175B ILE* 1.3 67.3 + - - +
176B ILE* 3.5 37.5 + - + +
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2B PHE* 3.7 39.0 - - + +
2B MET* 3.5 34.1 - - + +
3B VAL* 4.3 5.4 - - + +
150B PHE* 3.1 5.4 - - - +
151B SER* 2.9 45.2 + - - +
173B SER* 4.9 2.5 - - - +
174B MET* 1.3 75.7 - - - +
176B ILE* 1.3 64.5 + - - +
177B GLY 3.7 0.3 + - - -
178B GLY 3.0 23.6 - - - +
180B ASP* 4.5 5.2 - - + +
183B LEU* 4.0 27.6 - - + -
342B TYR* 4.0 5.6 - - - +
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2B PHE* 4.4 5.5 - - - -
2B MET* 3.8 15.8 - - - +
87B ILE* 4.8 9.4 - - + -
90B GLY* 5.3 1.8 - - - -
91B PRO* 3.9 31.6 - - + +
121B LEU* 6.2 1.8 - - + -
136B PHE* 6.4 0.7 - - + -
137B PHE* 3.7 16.2 - - + -
140B LEU* 3.5 32.1 - - + -
146B VAL* 3.7 11.4 - - + +
150B PHE* 4.0 13.2 - - + -
174B MET* 3.5 44.9 - - + +
175B ILE* 1.3 74.5 - - - +
177B GLY* 1.3 62.2 + - - +
178B GLY 3.5 1.3 + - - -
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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