Contacts of the strand formed by residues 137 - 145 (chain B) in PDB entry 3CMA
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 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B ALA* 4.1 22.7 - - + -
87B TYR 3.6 15.0 - - - +
88B GLU* 4.4 0.7 - - - +
89B ASP* 3.5 8.3 - - - +
97B LEU* 5.1 2.0 - - + -
128B ILE* 4.5 4.5 - - + -
131B ALA* 3.9 18.6 + - + -
132B HIS* 3.9 38.4 - - + +
135B GLY* 3.4 4.4 - - - +
136B ASP* 1.3 75.6 - - - +
138B GLY* 1.3 72.2 + - - +
140B LEU* 4.1 25.6 - - + -
171B VAL* 4.7 14.4 - - + +
175B LEU* 4.3 12.8 - - + -
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Residues in contact with GLY 138 (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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87B TYR 2.4 23.8 + - - -
88B GLU* 3.7 0.2 - - - +
89B ASP* 3.6 15.3 - - - -
94B GLN* 3.5 17.9 - - - -
136B ASP 3.4 3.4 + - - -
137B LEU* 1.3 78.4 - - - +
139B ASP* 1.3 62.1 + - - -
140B LEU* 5.4 0.2 - - - +
171B VAL* 5.1 8.3 - - - +
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Residues in contact with ASP 139 (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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87B TYR* 3.3 31.4 + - - +
94B GLN* 2.8 30.1 + - - +
137B LEU* 4.8 0.3 - - - +
138B GLY* 1.3 76.4 - - - -
140B LEU* 1.3 68.2 + - - +
141B ARG* 2.7 35.7 + - - +
165B ARG* 2.9 41.2 - - - +
174B ARG* 6.0 2.7 - - - +
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Residues in contact with LEU 140 (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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84B LEU* 4.4 16.4 - - + -
85B ARG 4.0 3.1 - - - +
86B ALA* 4.1 23.8 - - + -
128B ILE* 4.9 0.4 - - + -
137B LEU* 4.1 22.9 - - + -
138B GLY 5.4 0.4 - - - +
139B ASP* 1.3 85.1 - - - +
141B ARG* 1.3 58.1 + - - +
165B ARG* 3.6 1.0 - - - +
166B VAL* 2.7 46.6 + - + +
171B VAL* 4.0 9.4 - - + +
174B ARG* 4.1 17.3 - - + +
175B LEU* 3.5 47.8 - - + +
178B ALA* 5.5 0.2 - - + -
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Residues in contact with ARG 141 (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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26720 C 3.4 8.7 + - - -
26730 U 3.1 35.9 + - - -
26740 G 5.8 0.4 + - - -
29B TRP* 4.3 19.4 - - - +
84B LEU* 3.6 4.2 - - - +
85B ARG* 2.9 35.2 + - - +
87B TYR* 3.8 15.1 - - + -
94B GLN* 3.8 17.2 + - - -
139B ASP* 2.7 25.9 + - - +
140B LEU* 1.3 80.8 - - - +
142B LEU* 1.3 65.8 + - - +
163B GLU* 3.0 42.0 + - + +
164B THR 3.6 3.8 - - - +
165B ARG* 3.4 24.9 - - - +
166B VAL* 4.0 1.8 - - - +
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Residues in contact with LEU 142 (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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38B VAL* 3.7 32.3 - - + -
81B ALA* 3.6 24.2 - - + -
83B ALA 3.1 8.5 - - - +
84B LEU* 4.0 17.7 - - + -
141B ARG* 1.3 72.3 - - - +
143B ILE* 1.3 60.5 + - - +
144B THR* 3.0 21.5 + - - +
163B GLU* 4.5 2.0 - - - -
164B THR 3.0 29.6 + - - +
166B VAL* 3.5 13.9 - - + -
178B ALA* 4.1 10.1 - - + +
181B ILE* 4.1 11.9 - - + -
182B VAL* 3.4 31.4 - - + -
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Residues in contact with ILE 143 (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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26700 G 5.7 0.4 - - - +
26710 U 3.6 27.8 - - + +
81B ALA 3.5 1.0 - - - -
82B VAL* 2.8 30.0 + - + -
83B ALA* 2.8 34.5 + - + +
85B ARG* 4.1 25.1 - - + +
99B GLU* 4.2 10.3 - - - +
101B TRP* 4.6 17.7 - - + -
113B LEU* 6.1 0.9 - - + -
141B ARG 4.1 0.2 + - - -
142B LEU* 1.3 69.0 - - - +
144B THR* 1.3 62.0 + - - +
161B VAL* 3.7 24.2 - - + -
162B MET 4.1 2.7 - - - +
163B GLU* 3.7 15.7 - - + +
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Residues in contact with THR 144 (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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38B VAL* 5.5 1.2 - - - +
79B MET* 3.9 21.5 - - + -
80B ARG 3.2 14.6 - - - +
81B ALA* 4.0 2.3 - - - +
82B VAL* 5.7 0.4 - - - -
142B LEU* 3.0 22.0 + - - +
143B ILE* 1.3 75.0 + - - +
145B HIS* 1.3 63.9 + - - +
160B ASP 3.8 0.3 - - - +
161B VAL* 3.2 5.1 - - - +
162B MET* 2.6 51.9 + - - +
164B THR* 4.2 12.3 + - - -
188B HIS* 3.6 28.3 + - + +
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Residues in contact with HIS 145 (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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79B MET* 3.3 7.8 - - - +
80B ARG* 3.1 57.5 + - + +
82B VAL* 3.5 26.4 - - + +
106B HIS* 3.7 26.6 - - + +
109B LEU* 3.9 19.6 - - + +
144B THR* 1.3 78.9 - - - +
146B THR* 1.3 88.8 + - - +
147B VAL* 4.7 1.0 - - - +
159B PRO* 3.2 18.9 - - + +
160B ASP 3.3 6.1 - - - +
161B VAL* 3.7 24.2 - - + -
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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