Contacts of the strand formed by residues 160 - 164 (chain M) in PDB entry 2X1W
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 SER 160 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158M ASN 4.1 0.8 + - - -
159M VAL* 1.3 74.7 - - - +
161M LEU* 1.3 58.7 + - - +
169M ARG* 2.7 46.1 + - - +
170M PHE 3.7 8.1 - - - -
171M VAL* 4.5 10.3 - - - -
172M PRO* 4.9 0.2 - - - -
185M PHE* 4.0 3.4 - - - -
200M CYS* 3.6 3.1 - - - -
201M GLU* 2.7 42.5 + - - +
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Residues in contact with LEU 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148M ILE* 3.8 31.6 - - + -
160M SER* 1.3 73.1 - - - +
162M CYS* 1.3 66.7 + - - +
168M LYS 3.6 0.7 - - - +
169M ARG* 3.4 2.6 - - - -
170M PHE* 2.8 41.0 + - + +
185M PHE* 3.7 31.9 - - + -
187M ILE* 4.0 19.3 - - + -
192M ILE* 4.2 11.7 - - + -
198M VAL* 4.3 7.9 - - + -
199M PHE* 3.2 33.2 - - - +
200M CYS* 3.9 14.4 - - - +
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Residues in contact with CYS 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M SER* 4.4 0.2 - - - -
161M LEU* 1.3 74.0 - - - +
163M ALA* 1.3 61.8 + - - +
164M ARG* 5.6 1.8 - - - +
167M GLU* 6.4 1.6 - - + -
168M LYS 3.2 7.2 - - - +
169M ARG* 3.5 42.6 - - - -
198M VAL* 3.3 6.1 - - - +
199M PHE* 3.0 71.2 + - + -
201M GLU* 3.9 10.8 - - - -
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Residues in contact with ALA 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161M LEU* 5.8 0.4 - - + -
162M CYS* 1.3 73.9 - - - +
164M ARG* 1.3 64.1 + - - +
166M PRO 3.1 0.2 - - - +
167M GLU* 3.1 6.4 - - - +
168M LYS 2.8 33.0 + - - +
170M PHE* 4.4 15.3 - - + -
192M ILE* 4.6 2.7 - - + -
194M TYR* 3.3 20.0 - - + +
195M ALA* 3.8 8.1 - - + -
197M MET 3.5 5.6 - - - -
198M VAL* 3.7 19.7 - - + -
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Residues in contact with ARG 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASP* 3.4 15.8 + - - -
126B TRP* 5.5 0.5 - - - -
162M CYS* 5.6 1.8 - - - +
163M ALA* 1.3 78.6 - - - +
165M TYR* 1.3 99.9 + - + +
166M PRO 3.2 3.4 - - - -
167M GLU* 3.5 28.8 + - + +
195M ALA* 3.9 3.7 - - - +
196M GLY* 2.9 26.7 + - - -
197M MET* 3.2 44.8 + - + +
199M PHE* 3.9 31.8 - - + -
213M MET* 4.7 7.3 - - - +
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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