Contacts of the strand formed by residues 131 - 136 (chain B) in PDB entry 1CD9
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 LEU 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B CYS* 1.3 78.2 - - - +
132B TRP* 1.3 71.7 + - - +
133B LEU* 5.0 5.6 - - + -
174B PHE 3.8 0.5 - - - +
175B GLU* 3.7 3.3 - - - +
176B LEU* 3.0 38.9 + - + +
179B LEU* 3.7 22.7 - - + -
185B TYR* 4.7 4.9 - - + -
187B LEU* 4.2 23.8 - - + -
209B LEU* 3.7 32.8 - - + -
210B ARG 3.3 27.4 - - - +
211B PRO* 4.1 10.5 - - + -
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Residues in contact with TRP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 3.9 1.9 - - - +
117B LEU* 3.1 46.7 + - + +
119B ILE* 4.1 38.1 - - + +
127B GLN* 5.9 1.8 - - + -
130B CYS* 3.7 31.4 - - + -
131B LEU* 1.3 78.8 - - - +
133B LEU* 1.3 68.3 + - - +
173B GLN* 4.1 23.3 - - + +
174B PHE 3.5 2.9 - - - +
175B GLU* 3.3 50.5 + - + +
209B LEU* 5.0 0.7 - - - +
212B THR* 4.3 10.1 - - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 4.4 15.0 - - + -
115B GLN 3.8 11.0 - - - +
117B LEU* 3.8 3.8 - - - +
131B LEU* 5.0 5.8 - - + +
132B TRP* 1.3 84.1 - - - +
134B SER* 1.3 61.7 + - - +
135B TRP* 4.1 13.5 - - + -
150B LEU* 4.1 21.3 - - + -
173B GLN* 3.2 8.8 - - - -
174B PHE* 2.9 49.4 + - + +
176B LEU* 4.9 4.5 - - + -
187B LEU* 3.6 27.4 - - + -
207B LEU* 4.6 5.8 - - + -
209B LEU* 3.7 27.1 - - + -
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B MET 3.9 0.4 - - - +
114B LEU* 3.6 3.1 - - - +
115B GLN* 3.1 48.8 + - - +
117B LEU* 3.8 20.6 - - - -
133B LEU* 1.3 76.7 - - - +
135B TRP* 1.3 69.4 + - - +
136B LYS* 5.2 5.5 - - - +
171B LYS 3.4 10.8 + - - -
172B ASP* 3.4 17.3 + - - -
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Residues in contact with TRP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PRO* 5.1 3.4 - - + -
113B MET 3.3 13.5 - - - +
114B LEU* 3.9 11.9 - - + -
133B LEU* 4.1 7.6 - - + -
134B SER* 1.3 85.0 + - - +
136B LYS* 1.3 68.2 + - - +
148B CYS* 5.0 2.2 - - - -
167B LEU* 4.3 24.7 - - + -
168B PRO* 2.9 25.5 + - + -
169B SER 3.3 22.0 - - - -
170B SER* 3.3 10.1 - - - +
171B LYS* 3.1 50.3 + - + +
174B PHE* 3.6 48.9 - + + -
189B MET* 3.5 42.4 - - + -
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PRO* 3.5 5.1 - - - +
113B MET* 3.0 50.9 + - + +
115B GLN* 5.6 10.3 - - - +
134B SER* 5.2 5.8 - - - +
135B TRP* 1.3 79.8 - - - +
137B PRO* 1.3 76.8 - - + +
139B LYS* 6.3 1.3 - - - +
169B SER 4.0 3.4 - - - -
170B SER* 4.1 4.3 - - - -
172B ASP* 5.0 9.1 + - - -
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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