Contacts of the strand formed by residues 149 - 156 (chain B) in PDB entry 3CEI
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 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ALA* 4.1 6.3 - - + -
126B TYR 3.7 12.8 - - - +
127B ASN* 3.7 20.3 - - - +
128B LEU 5.4 0.2 - - - +
134B GLU* 2.6 36.1 + - - +
136B ILE* 3.6 19.7 - - + +
144B PRO* 3.2 17.9 + - + +
145B VAL* 3.4 16.3 + - - +
147B ASP* 3.2 27.4 + - + +
148B LYS* 1.3 81.9 - - - +
150B VAL* 1.3 62.7 + - - +
151B PRO* 3.4 11.0 - - - +
198B LEU* 3.8 4.7 - - - +
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Residues in contact with VAL 150 (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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125B ALA* 4.1 2.2 - - - -
126B TYR 2.7 35.7 + - - +
128B LEU* 3.6 24.7 - - + -
149B LYS* 1.3 74.3 - - - +
151B PRO* 1.3 74.4 - - - +
152B LEU* 3.4 3.5 + - - +
189B CYS* 4.5 3.6 - - + +
193B ALA* 3.6 30.1 - - + -
197B GLY 3.8 20.9 - - - +
198B LEU* 4.0 7.2 - - + +
200B SER* 3.7 15.5 - - - +
201B VAL* 3.8 13.2 - - + -
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Residues in contact with PRO 151 (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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71B TYR* 3.3 23.1 - - - +
75B PHE* 3.3 18.6 - - + -
123B TRP* 3.6 33.7 - - + -
124B ALA 4.0 4.7 - - - +
125B ALA* 4.3 4.7 - - + -
143B THR* 4.4 1.8 - - - +
144B PRO* 4.7 3.4 - - + -
145B VAL* 3.6 22.9 - - + +
149B LYS 3.4 9.9 - - - +
150B VAL* 1.3 91.7 - - + +
152B LEU* 1.3 64.9 + - - +
189B CYS* 3.7 7.3 - - - +
201B VAL* 4.0 4.3 - - + -
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Residues in contact with LEU 152 (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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75B PHE* 3.6 11.5 - - - -
79B CYS* 4.4 1.6 - - - -
91B LEU* 4.9 3.1 - - + -
124B ALA* 2.7 16.3 + - + +
126B TYR* 4.0 17.7 - - + +
133B ILE* 3.8 42.6 - - + -
150B VAL 3.6 13.9 - - - +
151B PRO* 1.3 78.0 - - - +
153B LEU* 1.3 64.7 + - - +
185B PHE* 4.7 0.2 - - - -
186B VAL* 3.5 34.7 - - + +
189B CYS* 3.6 12.2 - - - +
190B TYR* 3.5 43.5 - - + +
193B ALA* 4.3 1.6 - - + -
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Residues in contact with LEU 153 (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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75B PHE* 3.6 3.1 - - - -
79B CYS* 3.8 24.0 - - + -
105B PHE* 4.5 9.2 - - + -
109B PHE* 4.0 28.7 - - + -
122B ASN 4.6 0.2 - - - -
123B TRP* 3.2 6.3 - - - +
124B ALA* 2.9 37.4 + - + +
152B LEU* 1.3 80.9 - - - +
154B VAL* 1.3 67.8 + - - +
177B PHE* 3.9 10.5 - - + -
181B ILE* 3.8 34.1 - - + -
183B TRP* 4.4 15.3 - - + -
186B VAL* 3.8 19.3 - - + -
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Residues in contact with VAL 154 (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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72B ASN 4.2 5.2 - - - +
75B PHE* 3.6 20.0 - - + -
76B TYR* 3.7 31.1 - - + +
79B CYS* 3.6 6.7 - - - +
109B PHE* 4.7 1.1 - - - -
121B TRP* 3.8 23.1 - - + -
122B ASN 3.4 10.1 - - - +
123B TRP* 3.3 41.1 - - + -
153B LEU* 1.3 79.1 - - - +
155B VAL* 1.3 62.6 + - - +
177B PHE* 3.4 19.3 - - - -
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Residues in contact with VAL 155 (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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76B TYR* 4.0 3.4 - - + -
109B PHE* 3.9 12.1 - - + -
113B ALA* 3.9 11.4 - - + -
121B TRP* 3.6 1.9 - - - -
122B ASN* 3.0 45.2 + - + +
154B VAL* 1.3 80.0 - - - +
156B ASP* 1.3 65.7 + - - +
157B VAL* 3.6 3.6 + - + +
173B TYR* 3.7 15.3 - - + +
174B LEU* 3.9 15.9 - - + -
177B PHE* 3.6 41.3 - - + -
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Residues in contact with ASP 156 (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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26B HIS* 2.8 10.9 + - - -
73B HIS* 3.2 2.4 + - - -
76B TYR* 3.5 19.2 - - + -
120B GLY 3.7 0.9 - - - +
121B TRP* 3.4 28.7 - - + -
155B VAL* 1.3 70.7 - - - +
157B VAL* 1.3 64.6 + - - +
158B TRP* 3.2 26.4 + - - +
161B ALA* 3.8 16.7 - - + +
173B TYR* 2.8 32.2 + - - -
500B FE 1.9 32.4 - - - -
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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