Contacts of the strand formed by residues 177 - 182 (chain B) in PDB entry 3K7G
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 TRP 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PHE* 3.5 32.1 - + + +
53B SER 3.5 7.9 - - - -
54B PRO* 3.5 17.5 + - + -
56B VAL 2.9 23.4 + - - -
57B PRO* 4.9 0.7 - - + -
58B GLU* 3.3 56.0 - - + +
63B ALA* 3.7 18.2 - - + -
64B SER* 3.5 5.4 - - - +
175B PHE* 3.3 1.0 - - - +
176B ASP* 1.3 78.2 - - - +
178B VAL* 1.3 68.1 + - - +
179B TYR* 3.4 40.8 - + + -
187B HIS* 3.6 16.4 - + - -
188B CYS* 3.4 1.2 - - - +
189B SER* 2.9 41.0 + - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.0 4.1 - - + +
52B PHE* 3.1 4.3 - - - +
53B SER 2.8 34.3 + - - +
167B ALA* 3.5 27.4 - - + +
170B ALA* 3.8 7.6 - - + -
171B VAL* 3.8 34.3 - - + +
175B PHE* 3.8 22.9 - - + +
177B TRP* 1.3 81.3 - - - +
179B TYR* 1.3 64.1 + - - +
180B TYR 4.3 0.2 - - - -
186B VAL* 3.7 22.4 - - + -
187B HIS 3.4 3.6 - - - -
188B CYS* 4.3 2.9 - - - -
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 3.5 47.6 + - + +
51B GLN 3.5 10.5 - - - -
52B PHE* 3.9 14.4 - + + -
177B TRP* 3.4 38.1 - + + -
178B VAL* 1.3 76.6 - - - +
180B TYR* 1.3 60.8 + - - +
181B GLU* 2.8 53.9 + - + +
186B VAL* 3.6 3.7 - - - +
187B HIS* 2.8 40.5 + + + +
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.4 21.8 - - + +
48B ALA 3.3 29.4 - - - +
49B TYR* 3.5 20.6 - + + +
50B LYS* 2.8 28.4 + - - -
51B GLN 2.9 12.6 + - - +
160B ARG 3.9 16.5 + - - -
163B TYR* 3.9 12.6 - - + +
164B GLY* 3.6 29.3 + - - -
167B ALA* 4.7 3.4 - - + -
178B VAL 4.3 0.2 - - - -
179B TYR* 1.3 67.7 - - - +
181B GLU* 1.3 59.6 + - - +
182B SER 3.2 26.5 - - - -
183B LYS* 4.3 17.0 + - - +
185B HIS 4.0 6.1 - - - -
186B VAL* 4.5 10.5 - - + +
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Residues in contact with GLU 181 (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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49B TYR* 4.3 0.8 + - - -
50B LYS* 2.8 33.2 + - - +
139B HIS* 5.9 0.2 + - - -
152B ASP* 4.8 0.2 - - - +
179B TYR* 2.8 51.4 + - + +
180B TYR* 1.3 72.4 - - - +
182B SER* 1.3 60.8 + - - +
185B HIS* 2.7 38.0 + - + +
187B HIS* 3.7 12.8 + - + +
1001B ZN 3.8 8.7 - - - -
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 3.8 12.6 - - - -
180B TYR* 3.2 11.5 - - - -
181B GLU* 1.3 81.1 - - - +
183B LYS* 1.3 63.2 + - - +
184B ALA* 2.8 20.4 + - - +
185B HIS* 2.8 43.5 + - - +
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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