Contacts of the strand formed by residues 127 - 132 (chain B) in PDB entry 3LQM
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 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B VAL* 4.3 12.6 - - + -
121B GLU 3.6 2.7 - - - +
122B VAL* 3.4 33.2 - - + -
126B CYS* 1.3 79.7 - - - +
128B HIS* 1.3 63.6 + - - +
129B MET* 4.1 13.8 - - + +
176B GLU 3.9 0.7 - - - +
177B VAL* 3.4 3.6 - - - -
178B LEU* 2.9 37.1 + - + +
181B LEU* 3.8 15.0 - - + -
187B TYR* 4.1 28.7 - - + +
189B VAL* 4.1 21.8 - - + -
210B GLU* 4.3 11.9 - - + +
212B THR* 4.5 10.5 - - + -
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Residues in contact with HIS 128 (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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123A LEU* 3.8 7.3 - - + +
128A HIS* 2.9 40.7 + - + +
129A MET 4.1 19.9 + - - -
130A ARG* 5.1 0.6 - - - +
175A PHE* 4.2 13.7 - + - +
177A VAL* 4.8 1.6 - - + -
120B VAL* 3.3 2.6 - - - +
121B GLU* 2.7 38.0 + - + +
123B LEU* 3.9 23.3 - - + +
126B CYS* 3.4 31.8 - - - -
127B LEU* 1.3 75.3 - - - +
129B MET* 1.3 61.4 + - - +
176B GLU 3.7 3.4 - - - -
177B VAL* 3.6 27.8 - - + +
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Residues in contact with MET 129 (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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123A LEU* 4.0 3.4 - - - -
128A HIS* 4.4 2.1 - - - -
118B MET* 4.4 7.9 - - - +
119B GLN 3.1 11.2 - - - +
120B VAL* 3.9 12.1 - - + -
127B LEU* 4.1 20.0 - - + +
128B HIS* 1.3 73.9 - - - +
130B ARG* 1.3 61.4 + - - +
131B PHE* 3.6 32.5 - - + -
156B VAL* 4.1 18.8 - - - -
175B PHE* 3.3 7.0 - - - +
176B GLU* 3.0 40.4 + - + +
178B LEU* 3.9 33.0 - - + -
189B VAL* 4.1 18.8 - - + -
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Residues in contact with ARG 130 (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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123A LEU* 3.4 37.7 + - + +
124A ALA* 3.5 19.1 - - + -
125A ASP* 5.0 4.7 + - - -
126A CYS* 2.8 37.1 - - - +
128A HIS* 3.0 19.2 + - - -
177A VAL* 3.5 8.7 - - - +
179A ARG* 5.2 3.6 - - - +
215A ASP* 5.7 0.2 - - - -
218A VAL* 6.1 1.3 - - + -
118B MET* 3.3 5.5 - - - +
119B GLN* 2.9 35.4 + - + +
129B MET* 1.3 74.1 - - - +
131B PHE* 1.3 71.7 + - - +
132B LEU* 5.1 6.9 - - + +
174B ASP* 2.9 39.7 + - - +
175B PHE* 3.7 14.5 - - - +
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Residues in contact with PHE 131 (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 PRO* 4.9 0.2 - - + -
117B GLY 3.4 6.3 - - - +
118B MET* 3.9 18.2 - - + -
129B MET* 3.6 33.9 - - + -
130B ARG* 1.3 80.9 - - - +
132B LEU* 1.3 70.2 + - - +
146B LYS* 5.3 0.3 + - - -
154B TYR* 3.8 37.1 + + + -
156B VAL* 3.4 30.1 - - + -
171B PRO* 3.8 16.2 - - + -
174B ASP* 2.9 38.9 + - - +
175B PHE* 3.7 21.5 - - - -
176B GLU* 3.9 4.9 - - + -
191B VAL* 3.8 16.8 - - + -
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Residues in contact with LEU 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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124A ALA* 5.2 0.7 - - + -
215A ASP* 3.3 56.8 - - + +
218A VAL* 3.6 26.7 - - + -
116B PRO* 3.2 6.4 - - - +
117B GLY* 2.7 46.2 + - - +
130B ARG* 5.1 9.6 - - + +
131B PHE* 1.3 82.4 - - - +
133B ALA* 1.3 66.4 + - - +
135B LYS* 6.3 0.7 - - - +
154B TYR* 3.6 2.2 - - - -
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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