Contacts of the strand formed by residues 153 - 158 (chain K) in PDB entry 1VYH
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 153 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112K THR* 3.0 25.6 + - - -
126K ALA* 3.8 20.1 - - + +
127K SER 2.8 18.5 + - - +
130K ALA* 3.7 28.9 - - + +
131K THR 3.7 9.2 - - - +
132K ILE* 4.1 8.1 - - + -
149K HIS* 3.7 18.6 - - + -
152K SER* 1.3 75.9 - - - +
154K GLN* 1.3 60.0 + - - +
155K ASP 3.8 15.7 - - - +
156K ILE* 4.6 0.4 - - + -
167K SER* 4.1 15.5 - - - -
168K CYS 3.0 13.0 - - - +
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Residues in contact with GLN 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I ASP* 5.7 5.3 + - - +
112K THR* 3.3 21.3 - - + +
113K ARG* 2.9 35.8 + - - +
126K ALA* 5.1 0.2 - - - -
128K GLU* 4.3 13.5 + - - +
152K SER* 3.5 30.5 + - - -
153K VAL* 1.3 75.2 - - - +
155K ASP* 1.3 58.3 + - - +
168K CYS 2.7 10.9 + - - -
169K SER 3.9 0.3 - - - -
170K ALA* 3.5 10.9 + - - +
194K ASN* 3.3 27.4 + - - +
195K VAL 3.8 16.8 - - - +
196K SER* 4.1 15.0 - - - +
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Residues in contact with ASP 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ARG* 3.2 27.6 + - - +
115K ILE* 4.9 0.7 - - - +
153K VAL* 3.8 3.7 - - - +
154K GLN* 1.3 77.9 - - - +
156K ILE* 1.3 94.9 + - - +
167K SER* 3.5 0.7 - - - -
168K CYS* 3.1 28.4 + - + +
196K SER 4.1 0.4 - - - +
197K SER* 2.6 35.0 + - - -
198K VAL* 3.2 26.6 + - - +
241K ARG* 3.2 20.4 + - - -
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Residues in contact with ILE 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ARG* 4.4 6.8 - - + +
115K ILE* 3.4 44.4 - - + +
124K VAL* 3.6 21.8 - - + -
125K SER* 4.6 0.4 - - - -
126K ALA* 3.1 37.9 - - + +
132K ILE* 3.6 20.4 - - + -
153K VAL* 4.6 0.9 - - + -
155K ASP* 1.3 96.2 + - - +
157K SER* 1.3 68.9 + - - +
165K LEU* 3.4 22.0 - - + -
166K ALA 3.3 10.1 - - - +
167K SER* 4.7 2.2 - - - -
198K VAL* 4.2 2.2 - - - +
241K ARG* 5.3 1.2 + - - -
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Residues in contact with SER 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K ILE* 4.8 4.3 - - - -
156K ILE* 1.3 81.1 - - - +
158K PHE* 1.3 64.0 + - - +
165K LEU* 4.1 3.6 - - - -
166K ALA* 2.9 35.1 + - - -
198K VAL* 3.6 22.7 - - - -
199K SER* 3.3 6.9 - - - -
200K ILE* 2.8 34.3 + - - +
241K ARG* 5.5 1.6 - - - -
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Residues in contact with PHE 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K ILE* 3.6 36.1 - - + +
116K PHE 3.9 11.4 - - - +
117K HIS* 3.6 31.6 - + + -
118K PRO* 4.1 14.6 - - + -
124K VAL* 3.8 14.1 - - + -
157K SER* 1.3 80.5 + - - +
159K ASP* 1.3 68.0 + - - +
162K GLY* 4.4 7.2 - - - -
164K LEU 3.5 14.4 - - - -
165K LEU* 3.6 25.6 - - + -
179K PHE* 3.6 39.0 - + - -
200K ILE* 4.1 6.6 - - - +
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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