Contacts of the strand formed by residues 128 - 131 (chain I) in PDB entry 3VD1
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 GLU 128 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ALA 4.9 1.7 - - - +
210B PRO* 3.6 22.0 - - + +
211B ALA* 3.0 40.0 + - - +
212B SER 5.1 0.9 + - - -
126I HIS* 3.3 16.0 - - + +
127I PHE* 1.3 78.5 - - - +
129I VAL* 1.3 63.6 + - - +
130I THR* 4.1 8.3 + - - +
162I GLN 3.6 0.2 - - - +
163I ILE* 3.3 6.1 - - - +
164I LYS* 2.7 69.2 + - + +
166I SER* 4.9 0.5 + - - -
288I ARG* 3.2 16.2 - - - +
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Residues in contact with VAL 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I PHE* 4.0 19.7 - - + -
128I GLU* 1.3 76.1 - - - +
130I THR* 1.3 70.0 + - - +
131I PHE* 4.5 8.5 - - + -
161I ILE* 3.8 21.1 - - + -
162I GLN 3.2 11.7 - - - +
163I ILE* 4.6 2.5 - - + -
275I ILE* 4.5 11.4 - - + -
288I ARG* 3.5 36.6 + - + +
290I PHE* 4.0 22.2 - - + -
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Residues in contact with THR 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B TYR 4.9 12.6 - - - +
227B ASP* 5.1 13.5 + - + +
128I GLU* 4.1 8.3 + - - +
129I VAL* 1.3 78.0 + - - +
131I PHE* 1.3 87.6 + - - +
161I ILE* 4.0 1.6 - - - +
162I GLN* 2.9 44.3 + - - +
249I PHE* 4.8 14.8 - - + -
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Residues in contact with PHE 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I VAL* 4.5 7.0 - - + -
130I THR* 1.3 94.9 - - - +
132I GLN* 1.3 65.5 + - - +
133I GLN* 3.4 3.1 + - - -
142I TRP* 3.8 23.6 - + + -
144I TYR* 3.7 53.8 - + + -
151I LEU* 4.1 18.4 - - + -
159I CYS* 4.8 0.9 - - - -
160I PRO 4.3 8.7 - - - -
161I ILE* 3.5 24.2 - - + -
162I GLN* 4.2 3.4 - - - -
290I PHE* 3.5 41.1 - + - -
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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
------------------------------------------------------------
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