Contacts of the strand formed by residues 94 - 101 (chain B) in PDB entry 4B92
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 THR 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLY 3.4 7.9 - - - +
64B ASP* 4.0 10.7 - - + +
89B ALA* 2.8 30.7 + - + +
90B LEU* 3.3 27.0 + - - +
92B GLY 4.5 0.3 + - - -
93B GLY* 1.3 79.5 - - - +
95B THR* 1.3 60.4 + - - +
96B MET 3.1 27.1 - - - +
97B ILE* 4.1 0.4 - - + -
126B CYS* 4.6 0.2 - - - -
351B VAL* 4.4 7.9 + - + -
354B ARG* 2.9 29.5 + - - +
355B MET* 3.7 9.4 - - - +
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY* 3.2 33.2 + - - -
62B GLY 2.8 9.1 + - - -
63B ILE* 5.2 0.9 - - - +
90B LEU* 3.9 9.0 - - + -
94B THR* 1.3 77.2 - - - +
96B MET* 1.3 60.4 + - - +
126B CYS* 3.2 20.8 - - - +
127B ASP* 3.7 7.3 + - - +
401B ASP* 3.4 30.4 + - + +
403B VAL* 4.1 3.8 - - + -
439B THR* 3.9 18.8 - - + -
440B ILE 3.7 21.8 - - - +
441B SER* 4.4 4.0 + - - -
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 3.0 3.8 + - - -
63B ILE* 3.3 28.8 - - + -
64B ASP 2.9 24.0 + - - -
94B THR* 3.1 9.6 - - - +
95B THR* 1.3 80.8 - - - +
97B ILE* 1.3 70.6 + - - +
98B ILE* 3.9 16.2 - - + -
126B CYS* 4.2 0.2 - - - -
127B ASP* 3.5 13.0 - - + +
128B TYR* 3.8 27.1 - - - +
129B ALA* 4.0 6.3 - - + -
385B LEU* 5.0 0.2 - - - -
387B LEU* 3.6 25.6 - - + -
391B LYS* 3.6 29.8 - - + -
401B ASP* 5.2 0.2 - - - +
462B CYS* 4.1 13.0 - - + -
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Residues in contact with ILE 97 (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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64B ASP* 3.6 6.5 - - + -
67B THR* 3.7 30.5 - - + +
69B PHE* 3.9 24.5 - - + -
82B PHE* 4.2 13.0 - - + -
86B THR* 4.0 15.3 - - + -
89B ALA* 4.0 27.4 - - + -
94B THR* 4.1 3.4 - - + -
96B MET* 1.3 81.3 - - - +
98B ILE* 1.3 63.1 + - - +
99B GLY 4.1 7.6 - - - +
126B CYS* 4.2 4.9 - - - -
127B ASP 3.4 3.1 + - - +
128B TYR* 3.1 39.4 - - + -
129B ALA 3.2 1.9 + - - -
351B VAL* 4.8 0.7 - - + -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.5 1.8 - - + -
64B ASP 2.9 14.6 + - - +
65B THR* 3.8 14.7 - - + +
66B SER* 4.0 2.4 - - - -
67B THR* 3.0 27.2 + - - -
96B MET* 3.9 17.9 - - + -
97B ILE* 1.3 81.0 - - - +
99B GLY* 1.3 62.6 + - - +
129B ALA* 3.2 32.5 - - + +
130B LEU* 4.0 3.1 - - - +
131B HIS* 3.2 39.9 - - + +
156B SER* 5.3 0.2 - - - +
385B LEU* 3.9 31.6 - - + -
464B LEU* 5.4 1.1 - - + -
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Residues in contact with GLY 99 (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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67B THR* 3.7 10.1 - - - -
69B PHE 5.9 0.7 - - - -
82B PHE* 5.0 7.2 - - - -
97B ILE* 4.0 7.5 + - - +
98B ILE* 1.3 75.1 - - - +
100B HIS* 1.3 59.6 + - - -
129B ALA 2.6 16.3 + - - -
130B LEU* 3.3 15.7 - - - -
131B HIS* 2.7 35.5 + - - -
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Residues in contact with HIS 100 (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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66B SER* 3.2 24.9 + - - -
67B THR 3.2 17.9 + - - +
68B HIS* 3.4 41.5 - + + +
69B PHE 5.4 3.1 - - - +
71B GLN* 4.5 16.3 + - - +
82B PHE* 5.8 1.6 - - - -
99B GLY* 1.3 74.4 - - - -
101B VAL* 1.3 65.2 + - - +
102B LEU* 4.1 1.0 + - + -
116B CYS* 4.7 7.1 - - - -
130B LEU* 5.1 0.2 - - - -
131B HIS* 3.6 27.6 - + - +
158B GLN* 3.4 43.8 - - + +
160B PHE* 5.5 3.1 - + - -
189B ARG* 3.7 6.2 + - - -
325B ASP* 5.7 0.2 - - - -
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Residues in contact with VAL 101 (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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100B HIS* 1.3 80.9 + - - +
102B LEU* 1.3 58.8 + - - +
103B PRO* 3.3 5.1 - - + +
112B ALA* 3.6 40.2 - - + +
113B TYR* 3.9 7.9 - - - +
116B CYS* 3.9 27.6 - - + -
130B LEU* 4.1 17.5 - - + -
131B HIS 2.9 19.7 + - - +
132B VAL* 4.0 12.1 - - + -
133B GLY* 2.7 33.3 + - - -
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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