Contacts of the strand formed by residues 2168 - 2173 (chain B) in PDB entry 1V9P
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 ARG2168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2007B ARG* 6.1 0.4 - - - +
2079B PRO* 4.7 12.1 - - - +
2127B TYR* 2.6 44.1 + - + +
2128B TYR 3.7 4.7 - - - -
2129B GLU* 3.3 16.5 + - + +
2130B GLU* 5.2 2.7 - - - +
2166B PRO* 4.2 4.7 - - - +
2167B ASP* 1.3 85.7 - - + +
2169B LEU* 1.3 60.2 + - - +
2230B LEU* 3.5 41.1 - - + +
2231B GLY* 3.8 5.9 - - - -
2233B GLU* 5.0 2.0 - - - +
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Residues in contact with LEU2169 (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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2127B TYR* 3.7 7.8 - - - -
2128B TYR* 3.0 40.9 + - + +
2162B LEU* 4.1 20.6 - - + -
2165B VAL* 4.3 7.9 - - + -
2166B PRO* 4.1 18.4 + - + +
2167B ASP 3.9 1.0 - - - -
2168B ARG* 1.3 74.3 - - - +
2170B GLU* 1.3 67.9 + - - +
2171B VAL* 3.6 23.6 - - + -
2228B LEU* 3.4 33.2 - - + -
2230B LEU* 3.3 9.9 - - - +
2231B GLY* 4.1 8.5 - - - -
2246B TRP* 4.2 21.8 - - + -
2252B PHE* 4.7 0.2 - - + -
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Residues in contact with GLU2170 (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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2078B HIS* 4.1 0.5 - - - +
2079B PRO* 2.9 38.8 - - + +
2080B THR* 3.0 22.4 + - - +
2125B ASN* 3.1 20.1 + - - +
2126B LEU 3.6 4.0 - - - +
2127B TYR* 4.7 4.9 - - + +
2169B LEU* 1.3 76.5 - - - +
2171B VAL* 1.3 59.4 + - - +
2172B ARG* 2.7 40.0 + - - +
2228B LEU* 3.1 8.1 - - - +
2229B GLY 2.7 27.0 + - - -
2230B LEU* 2.7 28.4 + - + +
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Residues in contact with VAL2171 (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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2125B ASN* 3.5 1.6 - - - -
2126B LEU* 2.8 41.0 + - + +
2128B TYR* 3.8 6.5 - - + -
2169B LEU* 3.6 25.4 - - + -
2170B GLU* 1.3 71.7 - - - +
2172B ARG* 1.3 62.9 + - - +
2173B GLY 3.7 1.6 + - - -
2225B PHE* 3.2 27.7 - - + -
2227B ALA 3.7 6.5 - - - +
2228B LEU* 3.9 4.3 - - + -
2247B LEU* 3.7 18.8 - - + -
2252B PHE* 3.2 41.7 - - + -
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Residues in contact with ARG2172 (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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2080B THR* 2.7 42.1 + - - -
2081B ARG 3.0 21.8 + - - -
2082B MET* 3.4 29.1 - - + +
2124B VAL 4.1 4.9 - - - +
2125B ASN* 2.4 29.0 - - - +
2170B GLU* 2.7 17.5 + - - +
2171B VAL* 1.3 71.8 - - - +
2173B GLY* 1.3 61.2 + - - +
2225B PHE* 4.0 2.2 - - - -
2226B TYR* 2.9 28.2 - - + -
2227B ALA* 3.1 30.7 + - + +
2228B LEU 4.4 1.0 + - - -
2229B GLY* 3.7 24.4 - - - +
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Residues in contact with GLY2173 (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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2082B MET* 5.5 0.2 - - - +
2123B SER* 3.6 0.9 - - - -
2124B VAL* 3.4 24.3 + - - +
2171B VAL 3.7 1.4 + - - -
2172B ARG* 1.3 74.0 - - - +
2174B GLU* 1.3 70.9 + - - +
2224B THR 3.4 8.7 - - - -
2225B PHE* 3.2 33.7 - - - -
2226B TYR* 3.2 10.7 + - - -
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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