Contacts of the strand formed by residues 259 - 267 (chain B) in PDB entry 4BL8
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 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU 4.6 0.3 - - - +
113B ALA* 5.0 1.6 - - - -
156B TYR* 3.7 29.0 + - + -
159B TRP* 2.9 50.7 - + + -
160B PRO* 5.2 0.6 - - - +
168B TYR* 6.1 0.2 - - - -
169B ALA* 4.0 21.3 - - + -
257B LYS 3.6 2.6 + - - -
258B PRO* 1.3 72.5 - - - +
260B VAL* 1.3 63.0 + - - +
261B GLY 3.6 1.6 + - - -
329B GLU* 3.3 26.5 - - + +
330B ILE 4.3 2.5 - - - -
331B MET* 3.3 31.4 - - + +
332B PRO* 3.9 23.3 - - + -
337B MET* 5.0 2.0 - - + -
340B PHE* 4.2 12.1 - + - -
341B TRP* 3.7 20.2 - + + -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B HIS* 3.5 3.5 - - - -
111B VAL* 3.6 24.2 - - + -
112B GLU 3.3 15.9 - - - +
113B ALA* 4.4 3.8 - - + -
258B PRO 3.9 9.0 - - - +
259B PHE* 1.3 71.2 - - - +
261B GLY* 1.3 63.4 + - - +
262B VAL* 5.4 1.8 - - + -
325B ALA* 3.3 42.6 - - + +
329B GLU 2.9 18.5 + - - +
330B ILE* 3.8 15.6 - - + +
331B MET* 3.1 29.1 + - - +
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Residues in contact with GLY 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 4.6 4.5 - - - -
65B HIS* 3.7 1.1 - - - -
111B VAL 3.8 0.2 - - - -
112B GLU* 2.9 44.7 + - - +
156B TYR* 4.9 2.3 + - - -
259B PHE 3.6 3.0 + - - -
260B VAL* 1.3 75.9 - - - +
262B VAL* 1.3 63.9 + - - -
263B LEU 3.8 0.6 + - - -
331B MET* 3.3 22.4 - - - -
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 4.2 0.9 - - - -
65B HIS* 3.0 38.0 + - + +
93B PHE* 5.4 2.2 - - + +
94B THR* 4.6 14.1 - - + +
97B ALA* 3.7 23.6 - - + -
98B VAL* 5.1 0.2 - - + -
108B PRO* 3.8 25.8 - - + -
109B ILE 4.2 1.3 - - - +
110B ALA 3.3 12.6 - - - +
111B VAL* 4.2 19.3 - - + -
260B VAL* 5.4 2.0 - - + -
261B GLY* 1.3 74.8 - - - +
263B LEU* 1.3 74.1 + - - +
264B SER* 3.0 9.6 + - - +
304B ALA* 5.7 0.2 - - + -
330B ILE* 4.7 8.7 - - + -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 5.0 4.0 - - + -
16B LYS* 4.1 24.7 - - + +
62B PHE* 4.2 24.0 - - + -
63B TRP* 3.8 34.3 - - - +
64B ALA* 4.3 2.8 - - - +
109B ILE* 2.8 41.8 + - + +
110B ALA* 2.9 16.9 + - + +
112B GLU* 3.4 24.9 + - - +
261B GLY 3.8 3.2 + - - -
262B VAL* 1.3 69.7 - - - +
264B SER* 1.3 57.9 + - - +
300B LEU* 3.9 27.6 - - + +
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Residues in contact with SER 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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62B PHE* 3.3 7.3 - - - +
63B TRP 2.9 34.9 + - - +
65B HIS* 3.8 4.3 - - - +
68B PHE* 3.5 13.1 - - - -
98B VAL* 3.0 30.7 - - - +
106B ALA* 3.9 9.4 - - - -
107B TYR 3.3 10.4 + - - -
109B ILE* 4.3 3.1 - - - -
262B VAL* 3.0 16.7 + - - +
263B LEU* 1.3 75.1 + - - +
265B ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 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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60B ILE* 4.0 2.7 - - + -
61B ILE 3.5 5.4 - - - -
62B PHE* 3.6 37.0 - - + -
106B ALA* 3.4 3.7 - - - -
107B TYR* 2.9 42.2 + - + +
109B ILE* 4.5 4.5 - - + -
264B SER* 1.3 73.4 - - - +
266B GLY* 1.3 59.9 + - - +
267B ILE* 5.4 0.2 - - - +
281B LEU* 3.9 19.3 - - + +
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Residues in contact with GLY 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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60B ILE* 3.3 8.4 - - - +
61B ILE* 3.1 35.9 + - - +
68B PHE* 3.5 19.8 - - - -
77B LEU* 4.5 4.9 - - - -
80B ILE* 5.8 0.2 - - - -
105B ILE 3.9 5.8 - - - -
106B ALA* 3.8 8.7 - - - -
265B ALA* 1.3 74.3 - - - +
267B ILE* 1.3 64.3 + - - -
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Residues in contact with ILE 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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59B ASP 3.4 8.5 - - - +
60B ILE* 4.8 0.7 - - + -
77B LEU* 3.4 9.3 - - - +
78B ALA* 3.0 35.9 + - + +
80B ILE* 4.5 13.1 - - + +
105B ILE 4.7 2.8 + - - -
107B TYR* 4.5 12.6 - - + +
266B GLY* 1.3 75.7 - - - +
268B ASN* 1.3 76.4 + - - +
269B ALA 3.4 0.2 + - - -
271B SER* 4.5 2.2 - - - -
274B LYS* 3.9 37.0 - - + +
277B ALA* 3.8 25.8 - - + -
278B LYS* 4.2 9.2 - - + +
281B LEU* 4.1 16.4 - - + -
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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