Contacts of the strand formed by residues 309 - 314 (chain A) in PDB entry 3PEP
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 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A VAL 4.7 0.9 - - - +
267A TYR* 3.3 34.4 - + + -
268A PRO* 2.9 51.1 + - - +
269A LEU* 5.4 1.3 - - + -
305A PHE* 3.3 50.9 + + + +
306A ILE* 3.0 21.8 + - - +
307A ARG 3.4 0.6 - - - -
308A GLN* 1.3 92.7 - - + +
310A TYR* 1.3 56.8 + - - +
311A THR* 2.8 25.2 + - - +
322A LEU* 4.8 4.3 - - + -
323A ALA 3.4 7.9 - - - +
324A PRO* 3.6 36.2 - - + +
325A VAL* 3.8 2.9 - - - +
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Residues in contact with TYR 310 (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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152A SER* 2.7 30.8 + - - -
153A VAL 3.4 28.3 - - - -
154A TYR* 4.2 9.6 - + + +
166A LEU* 3.3 9.8 - - + +
170A ILE* 3.7 23.3 - - + -
171A ASP* 3.1 19.7 + - - +
174A TYR* 3.7 29.2 - + + -
175A TYR* 3.5 35.2 - + + -
179A LEU* 4.4 4.7 - - + +
309A TYR* 1.3 68.7 - - - +
311A THR* 1.3 59.7 + - - +
312A VAL* 4.0 8.1 - - + -
321A GLY 3.7 0.9 - - - +
322A LEU* 3.3 5.7 - - - -
323A ALA* 2.8 33.9 + - + +
325A VAL* 3.3 15.0 - - + +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER* 3.4 2.8 - - - -
153A VAL* 2.8 36.7 + - - +
214A VAL* 4.1 7.6 - - + +
305A PHE* 5.1 1.2 - - - -
306A ILE* 4.6 13.5 - - - +
309A TYR* 2.8 18.9 + - - +
310A TYR* 1.3 76.4 + - - +
312A VAL* 1.3 63.2 + - - +
313A PHE* 3.6 24.7 - - + -
320A VAL* 3.4 28.0 - - + -
321A GLY 3.3 5.8 - - - +
322A LEU* 4.0 16.6 - - + +
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Residues in contact with VAL 312 (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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150A LEU* 4.4 15.9 - - + -
151A PHE 3.5 9.0 - - - +
152A SER* 3.5 21.3 - - - -
170A ILE* 4.0 20.4 - - + -
179A LEU* 4.4 9.2 - - + -
181A TRP* 3.5 29.4 - - + -
310A TYR* 4.0 13.5 - - + -
311A THR* 1.3 73.6 - - - +
313A PHE* 1.3 70.1 + - - +
314A ASP 4.2 0.2 - - - +
320A VAL* 3.2 9.2 - - - +
321A GLY* 2.8 33.7 + - - +
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Residues in contact with PHE 313 (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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33A THR* 3.8 21.1 - - + -
150A LEU* 3.3 3.1 - - - -
151A PHE* 2.9 63.7 + + + -
153A VAL* 4.0 27.1 - - + -
190A TRP* 3.5 52.5 - + + -
214A VAL* 3.5 28.5 - - + -
216A THR* 4.7 5.2 - - - -
306A ILE* 5.2 1.8 - - + -
311A THR* 3.6 25.4 - - + -
312A VAL* 1.3 73.0 - - - +
314A ASP* 1.4 62.1 + - - +
315A ARG 3.4 2.0 + - - -
319A LYS 4.0 2.0 - - - -
320A VAL* 4.0 7.2 - - + -
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Residues in contact with ASP 314 (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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149A ASP 3.5 2.1 - - - +
150A LEU* 3.3 29.0 - - + +
181A TRP* 3.4 27.3 - - + -
190A TRP* 3.8 4.5 - - - -
312A VAL 3.8 0.8 - - - -
313A PHE* 1.4 70.6 - - - +
315A ARG* 1.3 59.1 + - - +
316A ALA* 3.0 24.4 + - - +
317A ASN* 3.0 24.4 + - + +
318A ASN* 3.1 21.1 + - - -
319A LYS 2.8 25.2 + - - +
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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