Contacts of the strand formed by residues 107 - 112 (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 TYR 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ILE* 3.7 33.6 - - + +
81B THR 4.7 1.2 + - - -
82B PRO* 4.0 11.7 - - + +
86B PHE* 3.8 22.0 - + - -
95B TRP* 4.1 7.4 - + - -
106B ALA* 1.3 71.0 - - - +
108B PRO* 1.3 68.5 - - + +
109B ILE* 3.7 7.1 + - + +
264B SER* 3.3 3.0 - - - -
265B ALA* 2.9 38.5 + - + +
267B ILE* 4.5 6.0 - - + +
278B LYS* 3.6 16.1 - - - +
281B LEU* 3.8 33.9 - - + -
282B GLU* 2.7 45.5 + - + +
286B LEU* 4.0 17.9 - - + -
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Residues in contact with PRO 108 (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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90B LEU* 3.7 25.8 - - + +
94B THR* 3.4 51.8 - - - +
95B TRP* 3.6 23.3 - - + +
98B VAL* 3.8 3.8 - - + -
106B ALA 3.6 8.5 - - - +
107B TYR* 1.3 85.9 - - + +
109B ILE* 1.3 64.8 + - - +
262B VAL* 3.8 8.1 - - + -
263B LEU 4.0 4.5 - - - +
264B SER* 4.1 6.5 - - - +
286B LEU* 4.0 5.4 - - - +
304B ALA* 4.0 4.0 - - + +
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Residues in contact with ILE 109 (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* 4.0 20.0 - - + -
107B TYR* 3.7 13.2 - - + +
108B PRO* 1.3 85.2 - - - +
110B ALA* 1.3 61.1 + - + +
262B VAL* 4.2 0.2 - - - +
263B LEU* 2.8 39.1 + - + +
264B SER* 4.2 2.0 - - - -
265B ALA* 4.2 6.1 - - + +
281B LEU* 5.5 1.1 - - + -
285B LEU* 4.3 18.6 - - + -
286B LEU* 3.9 23.8 - - + +
291B LEU* 4.0 22.2 - - + +
294B VAL* 6.3 0.2 - - + -
300B LEU* 4.2 12.1 - - + -
303B VAL* 3.6 7.1 - - - +
304B ALA* 3.0 21.3 + - - +
305B LEU 4.7 0.7 + - - -
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Residues in contact with ALA 110 (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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109B ILE* 1.3 86.4 - - + +
111B VAL* 1.3 65.7 + - - +
112B GLU* 3.9 0.7 + - - +
262B VAL* 3.3 6.8 - - - +
263B LEU* 2.9 31.1 + - + +
300B LEU* 3.2 44.9 - - + +
302B ALA 4.0 0.4 - - - +
303B VAL* 3.9 13.9 - - - +
304B ALA* 4.1 2.6 - - - +
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Residues in contact with VAL 111 (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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93B PHE* 3.8 31.9 - - + -
94B THR* 4.0 14.6 - - + -
110B ALA* 1.3 74.9 - - - +
112B GLU* 1.3 64.7 + - - +
260B VAL* 3.6 26.2 - - + -
261B GLY 3.9 2.2 - - - -
262B VAL* 4.2 10.1 - - + +
300B LEU 4.5 0.2 - - - -
301B GLY* 3.8 5.9 - - - -
302B ALA* 3.1 36.7 + - + +
303B VAL 5.6 0.4 - - - -
321B THR* 4.2 6.5 - - + +
322B MET* 4.2 24.5 - - + -
325B ALA* 4.8 4.0 - - + -
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Residues in contact with GLU 112 (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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16B LYS* 3.1 26.6 + - - -
64B ALA* 5.0 9.0 - - - +
110B ALA 4.5 3.4 - - - +
111B VAL* 1.3 77.7 - - - +
113B ALA* 1.3 65.2 + - - +
156B TYR* 4.5 9.4 + - - +
230B PRO* 4.7 6.1 - - + -
231B TRP* 3.3 37.0 - - + -
260B VAL* 3.3 6.9 - - - +
261B GLY* 2.9 41.7 + - - +
263B LEU* 3.4 24.7 - - + +
300B LEU 4.0 14.8 - - - +
321B THR* 4.6 0.2 - - - -
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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