Contacts of the strand formed by residues 94 - 102 (chain F) in PDB entry 3CHB
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 ARG 94 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLN* 3.0 43.4 + - - +
18F HIS* 3.4 29.4 + - - -
47F THR 4.0 3.8 + - - +
48F PHE* 3.3 19.4 - - + +
49F GLN 3.0 23.0 + - - -
87F VAL* 3.8 15.0 - - + -
88F TRP 3.5 13.0 - - - +
89F ASN* 4.1 16.2 + - - +
91F LYS 3.4 13.4 + - - +
92F THR* 4.0 0.2 - - - +
93F PRO* 1.3 71.3 - - - +
95F ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F GLN* 3.4 10.8 - - + +
51F GLU* 3.5 42.2 - - + +
87F VAL* 3.1 5.0 - - - -
88F TRP* 2.8 44.9 + - + -
91F LYS* 4.1 12.7 - - + +
93F PRO 3.3 0.8 + - - -
94F ARG* 1.3 70.8 - - - +
96F ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ILE* 3.8 20.6 - - + -
48F PHE* 3.8 20.9 - - + -
49F GLN 2.8 23.3 + - - +
50F VAL* 4.4 8.1 - - + +
51F GLU 5.7 0.5 + - - -
68F MET* 4.1 24.7 - - + -
72F LEU* 3.8 28.3 - - + -
85F LEU* 4.4 18.4 - - + -
86F CYS 3.8 4.0 - - - -
87F VAL* 4.2 3.6 - - + -
88F TRP* 3.6 4.3 - - - -
95F ALA* 1.3 71.0 - - - +
97F ALA* 1.3 60.6 + - - +
98F ALA 3.7 21.8 - - - +
31G LEU* 3.4 21.7 - - - +
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 5.7 0.4 - - + -
12F TYR* 6.2 0.7 - - + -
15F THR* 5.0 1.3 - - + -
68F MET* 4.5 0.2 - - - -
86F CYS* 2.8 33.5 + - - +
87F VAL 4.7 0.4 - - - +
88F TRP* 3.3 38.1 - - + -
95F ALA 3.4 1.0 + - - -
96F ILE* 1.3 74.6 - - - +
98F ALA* 1.3 59.9 + - + +
30G SER* 3.5 1.6 + - - -
31G LEU* 2.9 32.3 + - - +
32G ALA* 3.5 11.1 + - + -
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 3.6 23.8 - - + -
8F LEU* 4.3 9.4 - - + -
68F MET* 4.1 2.2 - - - -
85F LEU* 3.4 8.3 - - - +
86F CYS* 2.9 33.1 + - + +
96F ILE* 3.7 5.4 - - - +
97F ALA* 1.3 78.6 - - - +
99F ILE* 1.3 62.4 + - - +
28G THR* 5.2 1.3 - - + -
29G GLU 3.2 13.9 - - - +
30G SER* 3.9 13.0 - - - +
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Residues in contact with ILE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 3.6 4.0 - - - -
68F MET* 3.7 23.3 - - + -
71F THR* 4.3 15.5 - - + -
72F LEU* 3.7 27.1 - - + -
75F ALA* 5.5 2.0 - - + -
82F VAL* 4.0 22.4 - - + -
84F LYS 3.6 3.8 - - - -
85F LEU* 3.7 19.1 - - + -
98F ALA* 1.3 76.4 - - - +
100F SER* 1.3 71.7 + - - +
101F MET* 4.4 13.0 - - + -
27G TYR* 5.6 1.1 - - + -
28G THR* 3.2 4.7 - - - +
29G GLU* 2.9 46.0 + - + +
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Residues in contact with SER 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 3.7 13.1 - - - +
82F VAL* 3.7 3.5 - - - +
83F GLU* 2.7 54.8 + - - -
84F LYS* 3.0 31.3 + - - +
99F ILE* 1.3 74.0 - - - +
101F MET* 1.3 61.7 + - - +
26G SER* 6.0 1.6 - - - -
27G TYR 3.4 5.2 - - - -
28G THR* 3.4 18.6 - - - -
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Residues in contact with MET 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F THR* 4.1 19.3 - - + -
75F ALA* 4.1 16.8 - - + -
80F ALA* 4.0 24.0 - - - -
81F LYS 3.6 14.8 - - - +
82F VAL* 4.4 6.3 - - - -
83F GLU* 4.1 0.4 - - - +
99F ILE* 4.4 15.0 - - + -
100F SER* 1.3 78.4 - - - +
102F ALA* 1.3 60.1 + - - +
26G SER* 3.2 8.4 - - - -
27G TYR* 2.8 62.2 + - + +
73G ARG* 5.0 3.8 - - + -
76G TYR* 3.3 25.2 + - + -
77G LEU* 4.3 11.4 - - + -
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASN* 5.1 1.7 - - - +
81F LYS* 3.7 18.0 + - - +
83F GLU* 4.1 27.7 - - + +
101F MET* 1.3 75.8 - - - +
103F ASN* 1.3 88.4 + - - +
25G PHE* 3.8 19.5 - - + +
26G SER* 4.0 9.9 - - - -
76G TYR* 3.2 7.3 + - - -
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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