Contacts of the strand formed by residues 260 - 268 (chain B) in PDB entry 5V6Y
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 PHE 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU 4.5 0.7 - - - +
114B ALA* 5.0 1.0 - - - -
115B LEU* 6.2 0.6 - - - +
157B TYR* 3.6 30.3 + - + +
160B TRP* 3.3 45.0 - + + +
161B PRO* 5.0 1.0 - - - +
169B TYR* 5.7 0.2 - - - -
170B ALA* 3.6 24.7 - - + -
258B LYS 3.6 2.6 + - - -
259B PRO* 1.3 73.6 - - - +
261B VAL* 1.3 62.7 + - - +
262B GLY 3.6 1.7 + - - -
330B GLU* 3.2 31.2 - - + -
331B ILE 4.1 9.0 - - - -
332B MET* 3.5 23.8 - - + -
333B PRO* 4.3 9.4 - - + -
338B MET* 4.6 1.1 - - + -
341B PHE* 3.7 21.8 - + - -
342B TRP* 3.6 22.7 - + + -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B HIS* 3.4 5.7 - - - -
94B PHE* 5.0 10.1 - - + -
112B VAL* 3.8 22.7 - - + -
113B GLU 3.7 11.7 - - - +
114B ALA* 4.8 3.1 - - + -
259B PRO 3.7 12.6 - - - +
260B PHE* 1.3 70.5 - - - +
262B GLY* 1.3 63.2 + - - +
263B VAL* 5.4 0.7 - - + -
326B ALA* 3.4 42.4 - - + +
330B GLU 2.5 21.6 + - - +
331B ILE* 3.4 13.7 - - + +
332B MET* 2.9 26.6 + - - +
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Residues in contact with GLY 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 4.7 3.4 - - - -
66B HIS* 3.6 2.5 - - - -
112B VAL* 3.5 4.0 - - - +
113B GLU* 2.6 48.6 + - - +
157B TYR* 4.9 2.8 + - - -
260B PHE 3.6 3.6 + - - -
261B VAL* 1.3 74.1 - - - +
263B VAL* 1.3 60.8 + - - +
264B LEU 4.0 0.9 - - - -
332B MET* 3.6 21.5 - - - -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 4.2 1.8 - - - +
66B HIS* 3.0 33.1 + - + +
94B PHE* 4.5 15.0 - - + -
95B THR* 4.6 9.6 - - + -
98B ALA* 3.9 24.5 - - + -
109B PRO* 3.9 27.8 - - + -
111B ALA 3.2 15.5 - - - +
112B VAL* 4.3 15.9 - - + -
261B VAL* 5.4 0.7 - - + -
262B GLY* 1.3 76.3 - - - +
264B LEU* 1.3 61.2 + - - +
265B SER* 2.9 21.6 + - - +
331B ILE* 5.0 2.9 - - + -
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Residues in contact with LEU 264 (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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13B ILE* 5.2 4.5 - - + -
14B ASN* 6.5 0.2 - - + -
17B LYS* 4.2 24.0 - - + -
63B PHE* 4.4 18.4 - - + -
64B TRP* 3.7 29.6 - - - +
65B ALA* 4.3 3.8 - - - +
109B PRO* 3.8 0.2 - - - +
110B ILE* 2.7 45.4 + - + +
111B ALA* 2.8 19.5 + - + +
113B GLU* 3.3 29.4 + - + +
262B GLY 4.0 2.2 + - - -
263B VAL* 1.3 69.9 - - - +
265B SER* 1.3 53.0 + - - +
301B LEU* 3.7 30.1 - - + +
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Residues in contact with SER 265 (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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63B PHE* 3.3 9.7 - - - -
64B TRP 2.8 35.3 + - - +
66B HIS* 3.8 4.0 - - - +
69B PHE* 3.3 18.1 - - - -
99B VAL* 3.2 29.5 - - - +
107B ALA* 4.0 5.2 - - - -
108B TYR 3.3 10.8 - - - -
109B PRO* 4.1 0.3 - - - +
110B ILE* 4.5 0.7 - - - -
263B VAL* 2.9 18.5 + - - +
264B LEU* 1.3 73.6 + - - +
266B ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 266 (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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61B ILE* 4.0 5.6 - - + -
62B ILE 3.3 5.2 - - - -
63B PHE* 3.6 32.1 - - + -
107B ALA* 3.3 3.8 - - - -
108B TYR* 2.7 48.1 + - + +
110B ILE* 4.5 2.9 - - + -
265B SER* 1.3 73.2 - - - +
267B GLY* 1.3 59.7 + - - +
282B LEU* 4.0 19.4 - - + +
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Residues in contact with GLY 267 (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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61B ILE* 3.3 8.9 - - - +
62B ILE* 3.0 38.2 + - - +
69B PHE* 3.3 21.4 - - - -
78B LEU* 4.3 4.9 - - - -
106B ILE 4.0 5.6 - - - -
107B ALA* 3.9 7.2 - - - -
266B ALA* 1.3 74.9 - - - +
268B ILE* 1.3 61.7 + - - -
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Residues in contact with ILE 268 (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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60B ASP 3.5 9.0 - - - +
61B ILE* 4.8 0.7 - - + -
62B ILE* 5.8 0.2 - - - -
78B LEU* 3.3 8.7 - - - +
79B ALA* 2.8 38.8 + - + +
81B ILE* 4.3 13.3 - - + +
106B ILE 4.6 3.2 + - - -
108B TYR* 4.2 19.7 - - + +
267B GLY* 1.3 76.3 - - - +
269B ASN* 1.3 70.3 + - - +
272B SER* 4.9 3.1 - - - -
275B LYS* 4.3 25.4 - - + +
278B ALA* 3.9 31.2 - - + -
279B LYS* 4.2 13.7 - - + +
282B LEU* 4.3 11.4 - - + -
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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