Contacts of the strand formed by residues 134 - 137 (chain A) in PDB entry 1VHQ
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 LEU 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.3 31.4 - - + +
124A ALA* 4.0 16.8 - - + +
127A MSE 3.7 23.1 - - + -
128A HIS* 4.8 2.9 - - + +
132A LYS 4.2 4.3 - - - +
133A PRO* 1.3 83.2 - - - +
135A GLY* 1.3 54.3 + - - +
136A PHE* 3.8 20.0 - - + -
148A PHE* 3.7 33.2 - - + -
188A LYS 3.0 6.1 + - - +
189A ILE* 3.5 21.5 - - + +
190A VAL* 2.8 33.6 + - - +
215A VAL* 4.4 4.3 - - - -
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Residues in contact with GLY 135 (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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92A LEU 2.9 11.4 + - - +
93A ILE* 3.3 6.5 - - - -
94A VAL 2.8 30.6 + - - -
134A LEU* 1.3 74.9 - - - +
136A PHE* 1.3 61.9 + - - -
190A VAL 3.1 8.5 - - - -
211A LEU* 4.2 11.9 - - - -
215A VAL* 4.2 15.6 - - - +
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Residues in contact with PHE 136 (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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92A LEU* 5.3 3.8 - - + -
94A VAL* 3.7 26.9 - - + -
120A LEU* 5.4 3.8 - - + -
124A ALA* 4.9 4.3 - - + -
134A LEU* 3.8 31.4 - - + -
135A GLY* 1.3 83.2 - - - -
137A MSE 1.3 64.0 + - - +
140A ALA* 3.6 26.0 - - + -
141A PRO* 3.9 17.7 - - + -
143A MSE 4.2 14.4 - - + -
144A LEU* 3.8 32.1 - - + -
147A ILE* 4.2 18.6 - - + -
189A ILE* 5.0 1.1 - - + -
190A VAL 2.9 6.6 + - - -
191A THR* 3.1 34.5 - - + -
192A THR 3.3 1.6 + - - -
211A LEU* 3.7 2.1 - - - +
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Residues in contact with MSE 137 (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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24A GLU* 3.4 23.3 - - - +
28A THR* 3.5 22.0 - - + +
93A ILE* 3.7 24.7 - - + -
94A VAL 3.3 6.7 + - - +
95A PRO* 3.7 14.4 - - + -
96A GLY* 3.4 10.7 - - - +
136A PHE* 1.3 77.5 - - - +
138A CSO 1.3 73.2 + - - +
140A ALA* 3.0 17.8 + - - +
141A PRO* 3.6 2.7 - - - -
192A THR* 3.3 22.2 - - + +
194A ALA* 4.3 2.0 - - + -
208A ILE* 3.8 35.2 - - + -
211A LEU* 4.2 17.7 - - + -
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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