Contacts of the strand formed by residues 91 - 97 (chain I) in PDB entry 2C2V
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 ILE 91 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78I MET* 3.9 31.0 - - + -
79I ILE 4.2 1.3 - - - -
80I LEU* 3.9 13.8 - - + +
90I ARG* 1.3 69.0 - - - +
92I TYR* 1.4 60.0 - - - +
93I SER* 4.0 2.6 + - - +
113I THR* 3.6 21.2 + - - +
168I GLU* 3.2 24.8 + - + +
169I GLY* 5.2 5.3 - - - -
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Residues in contact with TYR 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I MET* 3.1 4.8 - - - +
79I ILE* 2.9 48.4 + - + +
81I GLY 5.0 1.8 - - - -
87I TYR* 3.0 43.9 - - + +
90I ARG* 3.4 42.2 + - + +
91I ILE* 1.4 71.7 - - - +
93I SER* 1.4 59.7 + - - +
94I LEU* 3.1 6.7 - - + +
111I PHE* 3.8 17.0 - + + -
113I THR* 3.8 25.1 - - + -
114I LYS 3.6 14.4 - - - -
115I ILE* 3.0 33.7 - - + +
155I MET* 4.2 14.4 - - + -
165I GLN* 4.3 2.8 - - - +
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Residues in contact with SER 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I THR* 5.2 4.9 - - - -
77I GLY 3.4 12.3 - - - -
78I MET* 4.4 4.5 - - - +
91I ILE 4.0 2.7 + - - -
92I TYR* 1.4 68.1 - - - +
94I LEU* 1.3 72.2 + - - +
111I PHE* 3.8 3.1 - - - -
112I VAL* 3.1 34.8 + - - +
113I THR* 3.2 20.3 + - - -
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Residues in contact with LEU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I THR* 3.3 23.0 - - - +
77I GLY* 3.2 17.1 + - - -
78I MET* 3.6 9.9 - - - +
79I ILE* 4.3 8.1 - - + -
92I TYR* 3.1 22.7 - - + +
93I SER* 1.3 84.4 - - - +
95I LYS* 1.3 67.2 + - - +
96I ILE* 4.3 7.9 - - + -
109I VAL* 3.9 15.5 - - + -
110I ARG 3.2 9.9 - - - +
111I PHE* 3.5 42.0 - - + -
112I VAL* 4.2 2.8 - - - +
148I LEU* 4.3 6.7 - - + -
151I LEU* 3.9 19.5 - - + -
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Residues in contact with LYS 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I GLU* 3.3 33.0 + - - +
74I ARG* 6.6 0.4 - - + -
75I TRP 3.4 8.7 - - - +
76I THR* 4.6 5.4 - - + +
94I LEU* 1.3 76.2 + - - +
96I ILE* 1.3 63.2 + - - +
108I PHE 4.1 0.2 - - - +
109I VAL* 3.6 0.9 - - - -
110I ARG* 2.8 67.6 + - - +
112I VAL* 3.3 35.7 - - + +
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Residues in contact with ILE 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I ARG* 3.8 2.6 - - - +
75I TRP* 2.8 45.6 + - + +
76I THR 4.0 2.2 - - - +
77I GLY* 3.6 32.5 - - - +
94I LEU* 4.3 5.6 - - + -
95I LYS* 1.3 81.1 - - - +
97I GLU* 1.3 63.0 + - - +
98I CYS* 4.8 3.4 - - - -
107I PRO* 3.8 21.5 - - + -
108I PHE 3.3 12.3 - - - +
109I VAL* 3.7 25.4 - - + -
144I ILE* 4.5 20.9 - - + -
147I VAL* 5.1 4.5 - - + -
148I LEU* 4.6 13.0 - - + -
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Residues in contact with GLU 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I THR* 3.6 16.9 - - + +
74I ARG* 2.9 39.7 + - + +
96I ILE* 1.3 74.9 - - - +
98I CYS* 1.3 68.9 + - - +
99I GLY* 3.8 5.6 + - - -
107I PRO* 3.1 19.6 - - - +
108I PHE* 3.0 48.8 + - + -
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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