Contacts of the strand formed by residues 173 - 182 (chain A) in PDB entry 2PV1
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A THR* 1.3 89.7 + - + +
174A LEU* 1.3 68.3 - - - +
233A TRP* 3.6 16.1 - - + +
234A GLY* 3.3 32.1 - - - +
235A ARG* 4.0 13.9 + - + +
273A LEU* 3.4 3.3 - - - +
274A ARG* 2.7 70.6 + - + +
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Residues in contact with LEU 174 (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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172A THR 5.0 4.5 - - - +
173A GLU* 1.3 84.4 - - - +
175A ASN* 1.3 60.2 + - - +
176A LEU* 4.0 23.1 - - + -
233A TRP* 3.3 6.8 - - - -
234A GLY 3.0 30.0 + - - +
236A ILE* 4.9 19.5 - - + +
247A LEU* 4.5 28.5 - - + +
250A ALA* 5.3 3.4 - - + +
270A VAL* 4.3 6.1 - - + -
272A ASP 3.6 3.4 - - - -
273A LEU* 3.0 34.1 - - + -
1B TRP* 3.3 13.0 - - + -
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Residues in contact with ASN 175 (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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174A LEU* 1.3 73.0 - - - +
176A LEU* 1.3 61.0 + - - +
230A GLN* 6.1 1.0 - - - +
232A GLY* 3.2 20.0 + - - +
233A TRP* 3.3 48.5 - - + +
270A VAL 3.6 0.2 - - - -
271A ASN* 2.8 60.0 + - - +
272A ASP* 2.9 21.6 + - + +
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Residues in contact with LEU 176 (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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174A LEU* 4.3 10.5 - - + -
175A ASN* 1.3 81.8 + - - +
177A SER* 1.3 64.4 + - - +
230A GLN* 4.0 0.2 - - - -
231A MET* 2.8 44.3 + - + +
232A GLY 3.2 8.6 + - - -
239A LEU* 3.6 22.2 - - + -
247A LEU* 3.7 20.0 - - + -
268A LEU* 4.7 9.4 - - + -
269A LYS 3.3 15.7 - - - +
270A VAL* 3.7 23.1 - - + -
271A ASN* 3.4 8.0 - - - +
1B TRP* 3.5 28.7 - - + -
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Residues in contact with SER 177 (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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176A LEU* 1.3 72.8 + - - +
178A HIS* 1.3 60.6 + - - +
212A PHE* 3.7 21.0 - - - -
213A GLY* 6.1 0.2 - - - -
228A GLY 3.7 14.5 + - - -
229A GLY 3.1 9.0 - - - -
230A GLN* 3.6 17.5 - - - +
231A MET* 4.3 2.2 - - - -
268A LEU* 3.2 7.8 - - - +
269A LYS 2.9 30.5 + - - +
271A ASN* 3.0 25.4 + - - -
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Residues in contact with HIS 178 (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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177A SER* 1.3 75.5 - - - +
179A ILE* 1.3 84.5 + - - +
180A LEU* 3.8 17.3 - - + -
212A PHE* 4.1 1.5 - - - -
216A ALA* 4.2 2.8 - - - +
220A SER* 4.2 2.8 + - - -
222A ASP* 4.1 14.6 + - + +
229A GLY* 2.8 28.7 + - - +
231A MET* 3.7 19.3 - - + -
243A PHE* 4.0 3.8 - + - -
266A HIS* 2.8 36.1 + + + -
267A ILE 3.3 7.6 - - - -
268A LEU* 3.7 16.6 - - + -
3B TYR* 4.6 2.6 + - + -
5B PRO* 3.5 36.6 - - + +
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Residues in contact with ILE 179 (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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178A HIS* 1.3 85.4 + - - +
180A LEU* 1.3 62.8 + - - +
181A ILE* 4.0 23.1 - - + -
202A ILE* 3.9 15.0 - - + -
212A PHE* 3.5 28.9 - - + +
215A LEU* 3.9 15.7 - - + +
216A ALA* 3.7 34.5 - - + +
220A SER* 3.5 16.2 - - - +
265A PHE 3.7 0.9 - - - +
266A HIS* 3.4 4.7 - - - -
267A ILE* 2.9 48.2 + - + +
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Residues in contact with LEU 180 (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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178A HIS* 3.8 13.6 - - + -
179A ILE* 1.3 74.8 - - - +
181A ILE* 1.3 72.1 - - - +
182A PRO* 3.6 13.5 - - + +
220A SER* 3.1 12.3 + - - -
221A ALA* 2.9 38.5 + - + +
222A ASP* 4.1 21.1 - - + +
263A VAL* 3.8 34.8 - - + +
265A PHE 3.5 14.4 - - - +
266A HIS* 3.9 22.9 - - + -
6B ASN 5.8 1.1 - - - +
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Residues in contact with ILE 181 (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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179A ILE* 4.0 9.0 - - + -
180A LEU* 1.3 79.2 - - - +
182A PRO* 1.4 69.1 - - + +
195A ALA* 3.7 34.9 - - + +
198A GLN* 3.8 24.2 - - + +
199A ALA* 4.1 23.3 - - + +
202A ILE* 3.6 25.1 - - + -
219A HIS 3.7 16.4 - - - +
264A GLY* 3.5 0.5 - - - -
265A PHE* 2.9 43.1 + - + +
267A ILE* 4.7 2.0 - - + -
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Residues in contact with PRO 182 (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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180A LEU* 3.6 8.4 - - + +
181A ILE* 1.4 91.6 - - + +
183A LEU* 1.3 69.2 + - - +
184A PRO* 4.8 0.9 - - - +
195A ALA* 4.2 5.4 - - - +
219A HIS 5.3 1.6 - - - +
221A ALA* 3.5 33.0 - - + +
263A VAL 3.5 10.5 - - - +
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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