Contacts of the strand formed by residues 284 - 291 (chain A) in PDB entry 2HV9
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 TYR 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN* 4.8 7.0 - - - -
141A PHE* 3.5 38.4 - + + -
144A HIS* 5.9 1.1 - + - -
174A VAL* 3.4 8.1 - - - +
175A PRO* 3.7 36.6 - - + -
176A SER* 4.9 1.0 - - - -
179A VAL* 6.1 0.2 - - - +
214A PHE* 3.5 30.2 - + - -
216A LEU* 5.0 5.9 - - - +
249A GLY* 4.1 0.9 - - - -
250A PHE* 3.1 52.5 + + + +
280A VAL* 3.7 28.5 - - + -
281A VAL* 3.5 7.4 + - - +
282A GLY 4.3 3.5 - - - +
283A ILE* 1.3 90.0 - - + +
285A GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 285 (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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173A THR* 3.3 4.9 - - - -
174A VAL* 2.9 40.1 + - + +
175A PRO 4.1 3.6 - - - +
176A SER* 3.4 28.1 + - - -
177A ARG 4.8 0.5 + - - -
228A VAL* 5.7 1.4 - - - +
230A PHE* 4.1 8.0 - - - -
247A ARG* 2.8 48.6 + - - +
248A LYS 3.5 12.9 - - - +
249A GLY* 4.1 7.6 + - - -
250A PHE* 3.8 7.1 - - - -
284A TYR* 1.3 76.0 - - - +
286A VAL* 1.3 61.4 + - - +
287A VAL* 3.9 13.8 - - + +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.4 8.5 - - + -
57A LEU* 3.6 29.2 - - + -
172A MET 3.7 7.0 - - - +
173A THR* 4.3 8.3 - - + -
246A GLU* 4.3 11.7 - - + -
247A ARG* 3.1 6.9 - - - +
248A LYS 2.7 42.0 + - - +
250A PHE* 4.1 17.7 - - + -
253A PHE* 4.2 29.4 - - + -
285A GLU* 1.3 72.7 - - - +
287A VAL* 1.3 69.6 + - - +
288A VAL* 4.3 7.4 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE 3.8 0.2 - - - -
172A MET* 3.0 49.2 + - + +
174A VAL* 4.0 14.1 - - + -
230A PHE* 3.9 18.6 - - + -
233A MET* 3.9 7.9 - - + -
244A LEU* 3.8 12.8 - - + -
246A GLU 3.1 3.1 - - - +
247A ARG* 4.5 1.8 - - + -
285A GLU* 3.9 20.6 - - + -
286A VAL* 1.3 84.4 - - - +
288A VAL* 1.3 63.7 + - - +
289A PHE* 3.3 32.1 - - + -
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Residues in contact with VAL 288 (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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57A LEU* 4.1 9.9 - - + -
61A TYR* 3.9 22.4 - - + +
169A TYR* 3.4 23.1 - - + -
170A PHE 3.6 6.7 - - - +
171A ILE* 3.6 26.0 - - + -
172A MET 4.8 0.2 - - - +
244A LEU* 3.5 6.4 - - - +
245A VAL* 2.8 44.0 + - + -
246A GLU* 2.8 23.1 + - + -
286A VAL* 4.3 3.4 - - + -
287A VAL* 1.3 80.1 - - - +
289A PHE* 1.3 67.5 + - - +
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Residues in contact with PHE 289 (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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169A TYR* 3.6 1.2 - - - -
170A PHE* 2.9 34.6 + + + +
172A MET* 3.7 17.0 - - + -
233A MET* 3.5 22.9 - - + -
234A VAL* 3.7 33.4 - - + -
237A PHE* 3.4 38.8 - + + -
242A LEU* 4.2 19.3 - - + -
243A SER 3.1 8.3 - - - -
244A LEU* 3.7 25.8 - - + -
245A VAL* 4.2 0.9 - - - -
287A VAL* 3.3 24.9 - - + -
288A VAL* 1.3 86.4 - - - +
290A ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 290 (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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164A LEU* 5.4 0.2 - - - -
167A GLY* 2.6 31.2 + - - +
168A GLY 3.1 12.6 - - - +
169A TYR* 3.5 43.5 + - + -
242A LEU* 3.2 4.1 - - - -
243A SER* 2.8 32.3 + - - -
245A VAL* 3.9 15.9 - - + +
289A PHE* 1.3 76.8 - - - +
291A LYS* 1.3 66.9 + - - +
292A LEU* 3.4 27.4 + - + +
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Residues in contact with LYS 291 (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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133A GLU* 4.5 5.1 + - - -
161A ALA* 3.1 22.2 + - - -
162A ARG* 5.2 0.6 - - - +
164A LEU* 2.8 51.5 + - + +
165A ARG 3.7 11.0 - - - +
166A PRO* 3.7 20.0 - - + +
167A GLY* 2.5 35.9 + - - -
168A GLY 2.9 10.0 + - - +
240A LEU 4.8 6.7 - - - -
241A GLY* 3.6 7.4 - - - +
242A LEU* 3.9 17.3 - - + -
290A ARG* 1.3 70.4 - - - +
292A LEU* 1.3 67.3 + - - +
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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