Contacts of the strand formed by residues 198 - 204 (chain M) in PDB entry 3V3K
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 PHE 198 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155M LEU* 5.9 0.9 - - + -
162M PRO* 3.8 21.8 - - - -
163M GLY 3.3 22.0 - - - +
164M HIS 3.7 13.0 - - - -
165M CYS* 3.8 17.0 - - + -
193M PHE* 3.1 27.5 + + + +
194M SER* 4.0 8.0 + - - +
196M LEU* 3.2 39.7 - - + -
197M HIS* 1.3 77.2 - - - +
199M MET* 1.3 61.0 + - - +
200M VAL* 3.0 14.7 + - + +
229M CYS* 3.9 22.9 - - + -
230M CYS 4.5 1.6 - - - -
231M VAL* 3.4 29.4 - - + -
400M PHE* 4.0 20.6 - + - -
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Residues in contact with MET 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M PRO* 3.7 26.4 - - + +
163M GLY 2.9 14.3 + - - +
164M HIS* 3.4 48.1 + - + +
165M CYS 3.2 17.6 + - - -
198M PHE* 1.3 66.8 - - - +
200M VAL* 1.3 64.5 + - - +
201M GLU* 3.7 4.2 + - - +
227M LEU* 3.6 28.3 - - + -
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Residues in contact with VAL 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M CYS* 3.4 18.8 - - + +
167M ILE* 3.8 20.9 - - + -
190M ARG* 3.6 30.2 - - + +
193M PHE* 3.6 16.6 - - + -
194M SER* 3.5 38.1 + - - +
198M PHE 3.0 10.0 + - - +
199M MET* 1.3 73.0 - - - +
201M GLU* 1.3 65.5 + - - +
202M VAL* 4.6 0.4 - - + -
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Residues in contact with GLU 201 (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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57B ARG* 6.0 0.2 + - - -
57D ARG* 4.6 17.4 + - - -
61D GLU* 6.0 3.4 - - - +
164M HIS* 5.9 1.2 + - - -
165M CYS 3.0 9.1 + - - +
166M LEU* 3.6 16.8 - - + +
167M ILE 3.1 22.3 + - - -
199M MET 3.7 4.0 + - - +
200M VAL* 1.3 75.6 - - - +
202M VAL* 1.3 69.1 + - - +
203M LYS* 3.2 29.6 + - + +
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Residues in contact with VAL 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M ILE* 3.5 16.4 - - + +
169M ASN* 4.8 4.0 - - + +
186M CYS* 3.4 34.1 - - - -
187M GLU* 5.1 3.8 - - - +
190M ARG* 3.8 37.7 - - + -
201M GLU* 1.3 78.1 - - - +
203M LYS* 1.3 70.6 + - - +
204M GLY* 4.1 8.0 + - - +
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Residues in contact with LYS 203 (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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55B CYS* 5.5 7.1 - - - -
57B ARG* 4.6 7.0 - - - +
166M LEU* 4.2 17.5 - - + +
167M ILE 2.9 12.3 + - - +
168M ILE* 3.5 6.3 - - + -
169M ASN 3.3 17.7 + - - -
201M GLU* 3.2 28.0 + - - +
202M VAL* 1.3 78.5 - - - +
204M GLY* 1.3 63.6 + - - +
205M ASP 4.0 0.2 + - - -
206M LEU* 3.7 29.5 - - + +
214M ALA* 3.5 37.9 + - + +
217M GLU* 4.2 14.6 + - - -
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Residues in contact with GLY 204 (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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169M ASN* 3.4 16.2 - - - -
202M VAL* 4.1 6.6 + - - +
203M LYS* 1.3 74.1 - - - +
205M ASP* 1.3 77.2 + - - +
206M LEU* 3.5 5.0 + - - +
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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