Contacts of the strand formed by residues 127 - 130 (chain G) in PDB entry 3CII
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 ALA 127 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121G TYR* 3.6 24.8 - - - -
122G SER 3.7 6.4 + - - +
125G HIS* 3.0 17.6 - - + +
126G THR* 1.3 81.1 - - - +
128G TRP* 1.3 70.7 + - - +
129G LEU* 3.5 15.5 + - + +
144G PHE* 5.1 11.2 - - + -
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Residues in contact with TRP 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G LEU* 4.1 9.2 - - + -
120G SER* 3.1 33.0 - - - -
121G TYR* 3.3 44.3 - + + -
127G ALA* 1.3 75.3 - - - +
129G LEU* 1.3 64.2 + - - +
136G LEU* 3.3 44.5 + - + +
144G PHE* 3.9 30.8 + + + -
147G PHE* 3.4 45.9 + + + +
148G ASN 4.1 6.5 - - - -
149G THR* 4.3 1.1 - - - -
151G ASN 3.3 25.4 - - - -
152G CYS* 4.8 0.9 - - - -
153G ILE* 3.8 30.5 - - + -
163G ASP* 5.7 0.2 - - + -
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Residues in contact with LEU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G LEU* 3.4 8.3 - - - +
120G SER* 3.0 33.2 + - - +
122G SER* 4.8 17.5 - - - +
124G GLU* 5.3 0.4 - - + -
125G HIS* 3.0 52.9 - - + +
127G ALA* 3.6 14.6 - - + +
128G TRP* 1.3 80.0 - - - +
130G TRP* 1.3 65.6 + - - +
133G GLY* 4.2 18.2 - - - +
134G SER 3.4 17.0 - - - +
135G ALA* 5.3 2.9 - - - -
136G LEU 4.9 0.4 - - - +
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Residues in contact with TRP 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LEU 3.8 7.6 - - - -
98G GLN* 3.5 33.4 - - + +
99G LEU* 3.5 41.7 + - + -
117G ILE* 4.1 7.4 - - + -
118G GLY 3.1 21.8 - - - -
119G LEU* 3.1 42.0 - - + +
120G SER* 4.9 2.9 + - - -
129G LEU* 1.3 80.1 - - - +
131G GLU* 1.3 67.6 + - - +
132G ASN* 3.2 15.9 - - - +
133G GLY* 3.5 7.4 + - - -
134G SER* 3.2 25.2 + - - +
135G ALA 3.4 22.0 + - - -
136G LEU* 3.8 19.4 - - + +
137G SER 4.8 1.6 - - - +
140G LEU* 4.2 10.3 - - + -
141G PHE* 4.2 7.4 - + - -
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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