Contacts of the strand formed by residues 162 - 171 (chain B) in PDB entry 5MWF
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 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.5 5.6 - - - +
45B LEU* 2.9 41.6 + - + +
46B SER 4.6 0.3 + - - -
147B GLU* 4.1 7.9 - - + -
148B ALA 3.7 12.3 - - - +
149B TRP* 3.5 38.5 - - + +
159B GLU* 3.5 24.0 + - + +
160B GLU 3.3 2.9 - - - +
161B LEU* 1.3 75.8 - - - +
163B ILE* 1.3 60.2 + - - +
164B GLU 3.7 18.6 - - - +
165B ARG* 3.5 35.9 - - + +
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.7 2.7 - - + -
39B ASN* 4.0 22.2 - - + +
43B GLU 4.0 3.4 - - - +
44B LEU* 3.7 20.6 - - + +
45B LEU* 3.4 24.9 + - - +
50B CYS* 4.2 1.3 - - - -
67B CYS* 4.0 18.8 - - + -
69B THR* 3.9 23.8 - - + +
148B ALA* 2.7 24.6 + - + +
149B TRP 3.8 22.4 - - - +
150B ASP* 3.9 6.3 - - - +
162B LEU* 1.3 73.2 - - - +
164B GLU* 1.3 63.2 + - + +
187B VAL* 3.7 20.1 - - + +
188B ALA* 4.8 4.5 - - + -
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.9 15.0 - - - +
146B VAL 4.6 0.4 - - - -
147B GLU* 3.2 3.6 - - - -
148B ALA* 2.7 36.1 + - + +
162B LEU* 3.7 7.5 - - - +
163B ILE* 1.3 82.7 - - + +
165B ARG* 1.3 79.4 + - - +
166B VAL* 4.0 16.8 - - + -
185B GLY* 3.2 9.2 - - - -
186B HIS* 3.0 15.8 + - - +
187B VAL* 2.8 29.9 + - - -
188B ALA* 3.1 30.9 + - + +
190B LEU* 4.5 6.7 - - + -
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Residues in contact with ARG 165 (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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45B LEU* 4.9 10.0 - - + +
84B PRO* 3.8 38.7 + - - +
145B ILE* 4.0 19.1 - - + +
146B VAL 3.5 3.8 - - - -
147B GLU* 2.7 38.8 + - + -
149B TRP* 4.8 0.6 - - - -
159B GLU* 2.8 28.7 + - - -
162B LEU* 3.5 26.8 - - + +
164B GLU* 1.3 85.6 + - - +
166B VAL* 1.3 71.8 + - - +
167B SER* 5.9 0.7 - - - -
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Residues in contact with VAL 166 (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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145B ILE* 3.5 6.2 - - - +
146B VAL* 2.8 57.5 + - + +
164B GLU* 4.0 18.8 - - + -
165B ARG* 1.3 79.8 - - - +
167B SER* 1.3 61.1 + - - +
183B PHE* 3.9 45.3 - - + -
184B SER 5.2 0.4 - - - +
185B GLY* 4.8 11.4 - - - +
190B LEU* 4.4 13.5 - - + -
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Residues in contact with SER 167 (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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82B VAL* 3.6 24.7 - - - +
144B LEU 3.2 6.1 - - - -
145B ILE* 3.6 24.7 - - - -
146B VAL* 6.3 0.2 - - - -
165B ARG* 5.9 1.1 - - - -
166B VAL* 1.3 78.0 - - - +
168B HIS* 1.3 63.5 + - - +
183B PHE* 3.9 10.1 - - - -
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Residues in contact with HIS 168 (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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82B VAL* 5.2 0.7 - - - -
142B PHE* 4.4 13.7 - + - +
143B THR* 3.8 2.4 - - - -
144B LEU* 3.0 38.5 + - + +
167B SER* 1.3 76.2 - - - +
169B ALA* 1.3 75.3 + - - +
170B GLY* 4.1 7.8 + - - -
179B LYS* 3.8 21.8 + - - -
181B LEU* 4.0 33.1 - - + +
183B PHE* 3.8 21.8 - - + -
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Residues in contact with ALA 169 (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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78B TYR* 3.9 18.1 + - + +
79B GLN 3.8 13.7 - - - +
82B VAL* 3.8 25.6 - - + +
142B PHE 3.7 4.7 - - - -
143B THR* 4.1 9.2 - - - +
168B HIS* 1.3 84.1 + - - +
170B GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 170 (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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78B TYR* 3.9 12.1 - - - -
141B SER* 3.6 4.3 - - - -
142B PHE* 3.2 39.3 + - - +
168B HIS* 4.1 13.9 + - - -
169B ALA* 1.3 74.9 - - - +
171B MET* 1.3 60.7 + - - +
179B LYS* 5.6 0.7 - - - -
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Residues in contact with MET 171 (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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140B ARG* 3.4 37.7 - - + +
141B SER* 4.4 6.5 - - - +
142B PHE* 4.0 1.7 - - - -
170B GLY* 1.3 73.9 - - - +
172B ILE* 1.3 70.2 + - - +
173B ASN* 4.2 23.3 - - - +
179B LYS* 4.0 15.5 + - - +
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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