Contacts of the strand formed by residues 162 - 171 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.6 4.6 - - - +
45A LEU* 2.8 45.5 + - + +
46A SER 4.6 0.3 + - - -
147A GLU* 4.2 7.9 - - + -
148A ALA 3.5 16.2 - - - +
149A TRP* 3.7 32.7 - - + +
159A GLU 3.7 15.0 + - - +
160A GLU 3.3 3.5 - - - +
161A LEU* 1.3 75.4 - - - +
163A ILE* 1.3 60.5 + - - +
164A GLU 3.6 19.7 - - - +
165A ARG* 3.5 38.1 - - + +
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 5.7 3.1 - - + -
39A ASN* 3.9 23.1 - - + +
43A GLU 4.0 5.8 - - - +
44A LEU* 3.8 19.7 - - + +
45A LEU* 3.4 24.2 + - - +
50A CYS* 4.1 1.3 - - - -
67A CYS* 4.0 18.6 - - + -
69A THR* 3.8 28.9 - - + +
148A ALA* 2.8 22.8 + - + +
149A TRP 3.9 17.3 - - - +
150A ASP 4.0 6.1 - - - +
162A LEU* 1.3 71.5 - - - +
164A GLU* 1.3 63.7 + - + +
187A VAL* 3.7 18.9 - - + +
188A ALA* 4.7 5.8 - - + -
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.0 14.6 - - - +
146A VAL 4.1 0.4 - - - +
147A GLU* 3.3 2.8 - - - -
148A ALA* 2.8 33.2 + - + +
162A LEU* 3.6 9.0 - - - +
163A ILE* 1.3 83.4 - - + +
165A ARG* 1.3 78.6 + - - +
166A VAL* 4.1 16.8 - - + -
185A GLY* 3.1 9.2 - - - -
186A HIS* 2.8 16.6 + - - +
187A VAL* 2.7 31.0 + - - -
188A ALA* 3.1 30.8 + - + +
190A LEU* 4.6 6.1 - - + -
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 5.1 6.8 - - + +
84A PRO* 3.7 39.7 + - - +
145A ILE* 4.0 17.9 - - + +
146A VAL 3.4 3.6 - - - -
147A GLU* 2.7 38.8 + - + +
149A TRP* 4.7 6.3 - - - -
162A LEU* 3.5 33.9 - - + +
164A GLU* 1.3 86.2 + - - +
166A VAL* 1.3 69.5 + - - +
167A SER* 6.0 0.9 - - - -
185A GLY* 5.5 0.5 - - - -
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 3.4 5.7 - - - +
146A VAL* 2.9 55.6 + - + +
164A GLU* 4.1 16.4 - - + -
165A ARG* 1.3 79.4 - - - +
167A SER* 1.3 62.0 + - - +
183A PHE* 3.8 46.9 - - + -
184A SER 5.0 0.4 - - - +
185A GLY* 4.5 14.4 - - - +
190A LEU* 4.3 14.4 - - + -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 3.8 29.9 - - - +
84A PRO* 6.1 3.6 - - - -
144A LEU 3.3 10.1 - - - -
145A ILE* 4.3 11.2 - - - -
165A ARG* 6.0 1.1 - - - -
166A VAL* 1.3 78.3 - - - +
168A HIS* 1.3 63.9 + - - +
183A PHE* 3.8 10.9 - - - -
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Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 5.1 0.9 - - - -
142A PHE* 4.2 17.4 - + - +
143A THR* 3.5 3.4 - - - +
144A LEU* 2.7 46.1 + - + +
167A SER* 1.3 78.3 - - - +
169A ALA* 1.3 72.9 + - - +
170A GLY* 3.9 14.4 + - - -
179A LYS* 3.6 19.5 + - - -
181A LEU* 3.9 32.7 - - + +
183A PHE* 3.8 20.3 - - + -
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.8 24.6 + - + +
79A GLN 4.0 6.3 - - - +
82A VAL* 3.5 29.2 - - + +
142A PHE 3.7 5.2 - - - -
143A THR* 4.0 8.1 - - - +
168A HIS* 1.3 83.3 + - - +
170A GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.9 11.0 - - - -
141A SER* 3.6 3.8 - - - -
142A PHE* 3.2 39.5 + - - +
168A HIS* 3.9 16.6 + - - -
169A ALA* 1.3 75.2 - - - +
171A MET* 1.3 61.2 + - - +
179A LYS* 5.9 0.2 - - - -
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Residues in contact with MET 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 3.4 24.9 - - + +
141A SER* 4.4 7.2 - - - +
142A PHE* 3.8 3.4 - - - -
168A HIS* 5.1 0.4 + - - -
170A GLY* 1.3 74.5 - - - +
172A ILE* 1.3 77.9 + - - +
173A ASN* 4.0 30.3 - - - +
179A LYS* 4.6 11.6 + - - +
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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