Contacts of the helix formed by residues 135 - 142 (chain D) in PDB entry 3C5C
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 LYS 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D GLY 2.9 24.3 + - - -
31D ALA 3.5 11.2 - - - -
99D SER* 3.5 20.8 + - - -
100D VAL* 3.5 8.8 - - - +
101D ASP* 3.7 18.7 + - - +
134D ASN* 1.3 90.1 + - - +
136D LEU* 1.3 56.7 + - - +
137D ASP* 3.1 14.4 - - - -
138D MET* 2.9 34.2 + - + +
163D VAL 3.1 0.8 + - - -
201D GDP 2.7 64.2 + - + +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 4.4 6.3 - - + -
133D GLY 4.9 0.4 - - - +
134D ASN 3.3 2.0 - - - -
135D LYS* 1.3 75.4 - - - +
137D ASP* 1.3 62.1 + - - +
138D MET 3.0 1.6 + - - -
139D ALA* 3.0 27.0 + - + +
142D ARG* 3.6 16.2 - - - +
162D GLU* 3.5 45.5 - - + +
163D VAL* 2.9 22.7 + - - +
164D SER* 4.2 2.9 - - - -
167D LEU* 4.9 11.4 - - + -
171D HIS* 5.9 2.7 - - + +
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Residues in contact with ASP 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LYS 3.5 5.5 - - - -
136D LEU* 1.3 72.9 - - - +
138D MET* 1.3 75.5 + - + +
139D ALA* 3.3 2.7 + - - -
140D GLN 5.2 0.3 + - - -
164D SER* 2.7 28.9 + - - +
166D CYS* 3.5 10.3 - - - -
167D LEU* 4.3 22.6 - - + +
201D GDP 2.8 41.6 + - - -
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Residues in contact with MET 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 4.8 1.1 - - - -
101D ASP* 4.4 21.5 - - + +
135D LYS* 2.9 23.2 + - + +
137D ASP* 1.3 106.3 - - + +
139D ALA* 1.3 53.2 + - - +
140D GLN 3.2 4.0 - - - -
141D TYR* 2.8 57.7 + - + +
142D ARG* 3.6 0.7 + - - -
201D GDP 3.4 26.9 - - + +
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 4.7 4.5 - - + -
136D LEU* 3.0 22.2 + - + +
137D ASP 3.3 3.0 + - - -
138D MET* 1.3 71.5 - - - +
140D GLN* 1.3 56.9 + - - +
141D TYR 3.1 5.4 - - - -
142D ARG* 3.2 51.3 + - - +
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Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASP 5.2 0.4 + - - -
138D MET 3.2 1.0 + - - -
139D ALA* 1.3 77.2 - - - +
141D TYR* 1.3 83.1 + - + +
142D ARG 3.6 1.3 - - - -
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Residues in contact with TYR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ASP* 3.3 23.5 - - + +
138D MET* 2.8 42.8 + - + +
140D GLN* 1.3 99.6 - - + +
142D ARG* 1.3 62.7 + - - +
143D GLN* 3.5 4.7 + - - +
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Residues in contact with ARG 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 3.7 20.3 - - + +
101D ASP* 4.5 0.7 - - - +
136D LEU* 3.6 18.0 - - - +
138D MET 3.6 2.7 + - - -
139D ALA* 3.2 33.2 + - - +
140D GLN 3.6 0.8 - - - -
141D TYR* 1.3 77.0 - - - +
143D GLN* 1.3 59.6 + - - +
144D VAL 2.7 50.8 + - - +
145D THR* 4.0 13.0 - - + +
146D LYS* 3.5 15.2 - - - +
162D GLU* 2.8 42.8 + - - -
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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