Contacts of the strand formed by residues 259 - 267 (chain A) in PDB entry 4BLB
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A GLU 4.1 1.0 - - - +
113A ALA* 4.7 1.0 - - - -
114A LEU* 6.1 0.4 - - - +
156A TYR* 3.5 35.0 + - + -
159A TRP* 3.3 46.8 - + + +
160A PRO* 5.1 0.6 - - - +
169A ALA* 3.7 24.5 - - + -
257A LYS 3.5 2.4 + - - -
258A PRO* 1.3 74.3 - - - +
260A VAL* 1.3 62.1 + - - +
261A GLY 3.6 0.2 + - - -
329A GLU* 3.4 22.7 - - + -
330A ILE 4.3 3.4 - - - -
331A MET* 3.4 32.8 - - + -
332A PRO* 4.1 11.9 - - + -
337A MET* 4.6 1.3 - - + -
340A PHE* 4.2 8.7 - + - -
341A TRP* 3.5 31.6 - + - -
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Residues in contact with VAL 260 (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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65A HIS* 3.6 1.2 - - - -
93A PHE* 5.8 2.7 - - + -
111A VAL* 3.6 26.2 - - + -
112A GLU 3.4 12.1 - - - +
113A ALA* 4.5 2.5 - - + -
258A PRO 4.0 7.0 - - - +
259A PHE* 1.3 70.3 - - - +
261A GLY* 1.3 63.9 + - - +
262A VAL* 5.2 2.2 - - + -
325A ALA* 3.3 41.3 - - + +
329A GLU* 2.7 24.1 + - - +
330A ILE* 3.5 20.6 - - + +
331A MET* 3.0 24.1 + - - +
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Residues in contact with GLY 261 (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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64A ALA* 4.6 4.0 - - - -
65A HIS* 4.0 0.4 - - - -
111A VAL* 3.6 1.9 - - - -
112A GLU* 2.7 51.3 + - - +
156A TYR* 4.5 2.0 + - - -
259A PHE 3.6 3.2 + - - -
260A VAL* 1.3 74.8 - - - +
262A VAL* 1.3 61.9 + - - +
263A LEU 3.9 0.7 - - - -
331A MET* 3.4 22.2 - - - -
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Residues in contact with VAL 262 (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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64A ALA* 4.1 1.3 - - - -
65A HIS* 3.0 33.4 + - - +
93A PHE* 5.0 3.4 - - + -
94A THR* 4.6 11.4 - - + -
97A ALA* 3.6 26.5 - - + -
108A PRO* 3.7 22.2 - - + -
109A ILE 4.4 0.2 - - - +
110A ALA 3.1 15.3 - - - +
111A VAL* 4.6 13.0 - - + -
260A VAL* 5.2 2.7 - - + -
261A GLY* 1.3 73.7 - - - +
263A LEU* 1.3 74.9 + - - +
264A SER* 2.8 20.7 + - - +
330A ILE* 4.1 11.0 - - + -
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Residues in contact with LEU 263 (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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12A ILE* 5.0 7.4 - - + -
16A LYS* 4.4 21.8 - - + +
62A PHE* 4.5 17.7 - - + -
63A TRP* 3.8 26.9 - - - +
64A ALA* 4.2 4.0 - - - +
109A ILE* 2.6 45.8 + - + +
110A ALA* 2.6 24.2 + - + +
112A GLU* 3.6 25.0 - - - +
261A GLY 3.9 2.6 + - - -
262A VAL* 1.3 71.2 - - - +
264A SER* 1.3 55.5 + - - +
300A LEU* 3.7 30.5 - - + +
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Residues in contact with SER 264 (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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62A PHE* 3.2 5.1 - - - +
63A TRP 2.8 40.9 + - - +
65A HIS* 3.9 3.7 - - - +
68A PHE* 3.5 10.3 - - - -
98A VAL* 3.2 29.7 - - - +
106A ALA* 4.1 8.7 - - - -
107A TYR 3.2 11.0 - - - -
108A PRO* 3.8 0.5 - - - +
109A ILE* 3.9 4.3 - - - -
262A VAL* 2.8 21.2 + - - +
263A LEU* 1.3 73.6 + - - +
265A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 265 (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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60A ILE* 4.0 6.1 - - + -
61A ILE 3.5 4.0 - - - -
62A PHE* 3.6 32.5 - - + -
106A ALA* 3.3 3.2 - - - -
107A TYR* 2.7 44.4 + - + +
109A ILE* 3.9 8.0 - - + +
264A SER* 1.3 72.3 - - - +
266A GLY* 1.3 59.0 + - - +
281A LEU* 3.8 20.9 - - + -
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Residues in contact with GLY 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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60A ILE* 3.2 6.5 - - - +
61A ILE* 2.8 39.9 + - - +
68A PHE* 3.6 19.2 - - - -
77A LEU* 4.2 4.5 - - - -
105A ILE 4.0 5.2 - - - -
106A ALA* 3.9 9.0 - - - -
265A ALA* 1.3 73.9 - - - +
267A ILE* 1.3 62.9 + - - -
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Residues in contact with ILE 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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59A ASP 3.4 8.7 - - - +
60A ILE* 4.6 1.6 - - + -
77A LEU* 3.5 8.0 - - - +
78A ALA* 2.8 42.5 + - + +
80A ILE* 4.2 12.2 - - + +
105A ILE 4.7 2.6 + - - -
107A TYR* 4.0 24.0 - - + +
266A GLY* 1.3 75.9 - - - +
268A ASN* 1.3 68.6 + - - +
269A ALA 3.3 0.2 + - - -
271A SER* 4.7 2.5 - - - -
274A LYS* 4.0 36.6 - - + +
277A ALA* 4.0 22.4 - - + -
278A LYS* 4.3 6.1 - - + +
281A LEU* 4.0 15.0 - - + -
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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