Contacts of the strand formed by residues 79 - 87 (chain B) in PDB entry 3F9C
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU 3.7 1.0 - - - +
71B MET* 3.3 6.1 - - - +
72B PHE 2.9 39.8 + - - -
78B GLY* 1.3 74.2 - - - -
80B PHE* 1.3 64.4 + - - +
81B LEU* 3.6 31.2 - - + -
177B VAL* 5.2 0.9 - - + -
180B ARG* 4.2 0.2 - - - -
228B GLU* 4.8 1.4 + - - +
231B GLN* 2.7 33.2 + - - +
232B ALA* 3.8 20.3 + - + -
235B LEU* 3.9 16.6 - - + +
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Residues in contact with PHE 80 (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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69B ASP* 4.6 0.7 - - + -
70B LEU 3.4 9.0 - - - -
71B MET* 3.7 21.3 - - + -
79B THR* 1.3 74.9 - - - +
81B LEU* 1.3 70.7 + - - +
157B ARG* 3.4 33.2 - - - -
177B VAL* 3.6 5.2 - - - +
178B GLU* 2.9 62.5 + - + +
180B ARG* 3.6 24.4 - - - +
187B THR* 3.8 9.2 - - - -
188B TYR* 3.6 36.1 - + - -
249B LEU* 3.6 24.0 - - + -
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Residues in contact with LEU 81 (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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69B ASP* 3.5 3.8 - - - +
70B LEU* 2.9 57.8 + - + +
79B THR* 3.6 22.0 - - + -
80B PHE* 1.3 78.4 - - - +
82B ARG* 1.3 72.8 + - - +
83B LEU* 3.9 23.3 - - + +
157B ARG* 3.8 8.3 - - - +
175B ALA* 4.0 7.6 - - + -
176B ALA 3.1 19.1 - - - +
177B VAL* 4.0 4.7 - - + -
232B ALA* 4.2 6.7 - - + -
235B LEU* 5.1 0.7 - - + -
236B ILE* 3.6 28.3 - - + -
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Residues in contact with ARG 82 (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 CYS* 3.5 16.2 - - - -
68B THR 3.5 6.5 - - - +
69B ASP* 3.0 39.1 + - - +
81B LEU* 1.3 76.3 - - - +
83B LEU* 1.3 60.8 + - - +
84B TYR* 3.4 28.5 + - + -
95B THR* 3.6 12.7 - - - +
96B LEU 3.4 22.2 + - - +
97B TRP* 4.1 2.0 + - - +
99B PRO* 4.0 12.3 - - - +
130B THR* 4.8 3.4 - - - +
134B TRP* 3.8 18.0 - - - -
157B ARG* 3.5 20.7 - - + +
158B THR* 3.4 34.2 + - - +
174B VAL 3.5 1.4 - - - +
175B ALA 3.7 0.3 - - - -
176B ALA* 2.7 42.3 + - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B CYS* 3.1 9.9 - - - -
68B THR* 2.9 48.2 + - + +
69B ASP 6.0 0.4 - - - -
70B LEU* 6.1 2.0 - - + -
81B LEU* 3.9 21.9 - - + +
82B ARG* 1.3 72.2 - - - +
84B TYR* 1.3 60.6 + - - +
85B TYR* 3.3 33.6 - - + -
173B ILE* 3.6 30.1 - - + -
174B VAL 3.3 12.8 - - - +
175B ALA* 4.0 9.6 - - + -
236B ILE* 5.0 10.1 - - + -
253B PHE* 5.4 0.7 - - + -
255B MET* 5.9 2.7 - - + -
258B LEU* 4.5 23.8 - - + -
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Residues in contact with TYR 84 (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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65B VAL* 4.3 1.3 - - + -
66B GLY 3.5 5.6 - - - +
67B CYS* 3.7 26.9 - - + -
82B ARG* 3.4 24.3 + - + -
83B LEU* 1.3 71.6 - - - +
85B TYR* 1.3 62.9 + - - +
130B THR* 5.4 2.2 - - + -
132B ALA* 5.0 0.9 - - + -
157B ARG 4.2 1.7 + - - -
158B THR* 4.0 10.0 + - - -
160B TYR 4.4 3.3 - - - -
161B SER* 3.3 38.7 + - - -
164B GLY* 3.6 40.2 - - - +
165B ILE* 3.9 19.3 - - + -
168B ALA* 3.9 7.0 - - + -
172B PHE 3.9 0.7 - - - +
173B ILE* 3.5 2.9 - - - +
174B VAL* 2.8 47.8 + - + +
176B ALA* 4.2 20.9 - - + -
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Residues in contact with TYR 85 (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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65B VAL* 3.4 5.0 - - - -
66B GLY* 2.9 43.3 + - - -
67B CYS* 3.4 28.1 + - - -
68B THR* 3.7 8.7 - - + -
83B LEU* 3.3 30.1 - - + -
84B TYR* 1.3 76.2 - - - +
86B PRO* 1.3 83.1 - - + +
87B SER* 3.1 0.4 + - - -
135B ASN* 3.6 3.5 - - - -
136B SER 2.6 40.5 + - - -
137B PRO 4.0 7.9 - - - -
138B LEU* 3.7 18.8 - - + -
168B ALA* 3.7 7.0 - - - +
172B PHE 4.0 1.3 - - - -
173B ILE* 4.1 5.2 - - + -
253B PHE* 3.1 28.7 - + - -
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Residues in contact with PRO 86 (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 TYR* 3.6 24.2 - - + -
64B SER 3.3 7.6 - - - +
85B TYR* 1.3 84.7 - - + +
87B SER* 1.3 58.8 - - - +
138B LEU* 3.4 10.1 - - + +
139B ARG* 2.8 20.9 + - + -
144B TYR* 3.7 26.9 - - + +
168B ALA 3.5 17.5 - - - +
171B GLY* 3.6 19.1 - - - -
172B PHE 3.2 17.3 - - - +
173B ILE* 4.1 7.6 - - + -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 5.7 0.9 - - - -
64B SER* 2.7 28.5 + - - +
65B VAL 3.3 8.3 + - - -
66B GLY* 3.2 31.7 + - - -
85B TYR* 3.1 2.8 + - - -
86B PRO* 1.3 73.3 - - - +
88B GLN* 1.3 63.2 + - - +
89B ASP 3.2 15.2 + - - -
136B SER* 3.7 10.4 + - - -
137B PRO 3.2 13.7 - - - -
139B ARG* 3.7 13.7 - - - +
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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