Contacts of the strand formed by residues 104 - 108 (chain A) in PDB entry 2C0O
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 GLU 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLU 4.7 0.9 - - - +
76A LEU* 3.9 6.0 - - - +
87A LEU* 3.9 15.1 - - + +
95A LYS* 4.4 17.3 + - - -
96A ALA 3.5 4.0 - - - +
97A ARG* 3.0 46.5 + - + +
102A ARG 3.7 3.5 + - - +
103A LYS* 1.3 77.5 - - - +
105A GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 3.3 12.3 - - - -
76A LEU* 3.6 14.0 - - - +
95A LYS* 3.4 9.7 - - - +
96A ALA* 2.8 34.5 + - - +
104A GLU* 1.3 76.4 - - - +
106A TYR* 1.3 71.1 + - - -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 2.8 49.4 + - + -
75A ASP* 3.1 16.8 - - + +
76A LEU 2.8 28.4 + - - +
88A GLU* 4.5 7.5 + - - -
90A SER* 5.1 1.1 - - - -
93A TRP* 3.8 26.2 - - + -
94A TRP 3.3 15.9 - - - -
95A LYS* 3.6 39.5 - - + +
105A GLY* 1.3 73.7 - - - -
107A ILE* 1.3 66.5 + - - +
108A PRO* 4.8 0.2 - - - +
231A LYS* 4.4 32.0 - - + +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 4.7 8.5 - - + -
76A LEU* 4.1 9.0 - - + -
78A PHE* 3.7 22.9 - - + -
84A MET* 3.8 29.6 - - + -
86A VAL* 5.3 1.3 - - + -
93A TRP* 3.4 6.8 - - - -
94A TRP* 2.9 51.4 + - + +
96A ALA* 3.6 22.9 - - + -
106A TYR* 1.3 82.2 - - - +
108A PRO* 1.3 74.3 - - + +
112A VAL* 4.1 24.0 - - + -
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Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.9 28.3 - - + -
78A PHE* 4.3 16.6 - - + -
92A GLU 3.6 7.6 - - - +
93A TRP* 3.7 22.2 - - + -
107A ILE* 1.3 85.4 - - + +
109A SER* 1.3 63.9 + - - +
110A ASN* 3.1 19.5 - - - +
111A TYR* 3.0 26.2 + - + +
112A VAL* 3.8 7.6 - - - +
228A PRO* 3.8 13.9 - - + -
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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