Contacts of the strand formed by residues 263 - 267 (chain A) in PDB entry 3I5Y
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 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 3.0 40.9 + - + -
141A LEU* 4.2 10.9 + - + +
165A PRO 5.6 1.3 - - - -
166A ILE* 4.9 15.7 - - + -
169A HIS* 3.5 50.9 + + + -
182A LYS 3.1 7.2 + - - +
183A ALA* 3.3 11.6 - - + -
184A VAL 3.0 23.2 + - - -
261A VAL* 3.6 8.0 - - - +
262A ASP* 1.3 82.9 - - + +
264A LYS* 1.3 61.3 + - - +
265A VAL* 5.3 0.7 - - + -
299A ILE* 4.2 0.4 - - - -
300A LYS* 3.4 36.9 + - + +
302A LEU* 4.0 23.6 - - + -
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 3.2 11.7 - - + +
186A VAL* 6.1 2.7 - - + -
261A VAL* 5.2 0.4 - - + -
263A TYR* 1.3 74.8 - - - +
265A VAL* 1.3 63.4 + - - +
266A LEU* 4.2 10.3 - - + -
281A LEU* 5.9 2.5 - - + -
284A ILE* 5.6 3.4 - - + -
285A SER* 3.5 27.5 + - - +
288A LEU* 4.6 23.3 - - + -
289A ASN* 4.9 2.0 + - - -
299A ILE* 3.8 20.7 - - + +
300A LYS 3.0 7.7 + - - +
301A THR* 2.7 37.9 + - + +
302A LEU* 2.9 24.8 + - - +
319A ILE* 2.8 30.8 + - - -
321A ASN* 4.5 7.5 - - - +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 4.1 27.6 - - + -
166A ILE* 3.9 24.9 - - + -
184A VAL 2.8 10.5 + - - +
185A ILE* 4.1 22.2 - - + -
186A VAL* 2.8 32.6 + - - +
263A TYR* 5.3 2.0 - - + -
264A LYS* 1.3 75.1 - - - +
266A LEU* 1.3 73.6 + - - +
267A ASP* 4.0 3.6 - - - +
302A LEU* 3.5 36.6 - - + +
304A PHE* 4.7 2.5 - - + -
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Residues in contact with LEU 266 (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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186A VAL* 3.9 6.7 - - + -
264A LYS* 4.2 21.8 - - + -
265A VAL* 1.3 79.7 - - - +
267A ASP* 1.3 62.0 + - - +
269A ALA* 3.6 7.7 - - + +
272A LEU* 3.9 19.1 - - + -
273A LEU* 4.4 10.8 - - + -
281A LEU* 3.4 40.6 - - + -
301A THR* 4.3 1.8 - - + -
302A LEU 2.8 9.0 + - - +
303A LEU* 3.7 23.8 - - + -
304A PHE* 3.1 26.0 + - - +
319A ILE* 3.7 25.4 - - + -
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Residues in contact with ASP 267 (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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158A LYS* 5.3 2.9 - - - +
159A THR* 4.9 1.9 + - - -
162A PHE* 4.1 22.1 - - + -
185A ILE* 5.1 0.4 - - + -
186A VAL 3.2 14.5 + - - +
187A ALA* 4.7 4.7 - - + -
188A PRO* 3.7 3.8 - - - +
192A LEU* 4.2 8.9 - - - +
196A ILE* 3.7 28.4 - - + +
265A VAL* 3.7 5.5 + - + +
266A LEU* 1.3 70.6 - - - +
268A GLU* 1.3 91.0 + - + +
272A LEU* 3.2 15.8 - - - +
304A PHE* 3.9 15.6 - - - +
305A SER* 5.4 0.2 - - - -
900A MG 3.8 21.6 - - - -
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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