Contacts of the strand formed by residues 208 - 213 (chain A) in PDB entry 1P39
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 MET 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE* 4.0 11.4 - - - -
176A TRP* 2.8 54.3 + - + +
177A ARG* 5.1 1.6 - - - -
178A CYS 5.2 0.9 - - - +
195A LYS* 3.7 26.5 - - + -
196A MET 3.0 22.2 - - - +
197A LEU* 4.4 9.9 - - + -
198A GLN* 3.8 4.0 - - - +
206A ALA 3.2 25.8 - - - +
207A GLU* 1.3 77.4 - - - +
209A ARG* 1.3 70.2 + - - +
232A TYR* 3.6 38.1 - - + -
236A MET* 4.2 11.2 - - + -
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Residues in contact with ARG 209 (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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41A LYS* 4.1 1.0 - - - +
42A LEU* 3.7 19.4 - - - +
45A GLY* 5.3 5.4 - - - -
46A GLU* 5.6 1.7 + - - -
136A ILE* 5.9 2.6 - - - +
137A SER 3.5 17.8 + - - -
138A ASP* 2.7 34.8 + - - +
173A SER* 4.0 18.3 + - - +
174A LEU 3.3 5.9 + - - +
175A LYS* 3.5 16.4 - - - +
194A ASN 3.2 2.1 - - - +
195A LYS* 3.7 1.9 - - - -
196A MET* 2.8 57.2 + - + +
198A GLN* 2.8 33.6 + - - +
207A GLU* 3.0 25.1 + - - -
208A MET* 1.3 78.9 + - - +
210A LEU* 1.3 60.5 + - - +
211A LEU* 3.5 9.5 + - + -
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Residues in contact with LEU 210 (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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172A SER* 3.4 2.9 + - - +
173A SER* 3.2 4.0 - - - -
174A LEU* 2.8 52.0 + - + +
176A TRP* 4.2 16.7 - - + +
190A ILE* 4.0 17.3 - - + -
191A PRO* 3.1 41.7 - - + +
193A GLY* 3.7 25.8 - - - +
194A ASN 3.5 1.1 - - - +
195A LYS* 3.6 32.8 - - + +
208A MET 4.2 0.2 - - - -
209A ARG* 1.3 69.6 - - - +
211A LEU* 1.3 60.7 + - - +
212A SER* 4.0 8.8 + - - +
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Residues in contact with LEU 211 (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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12A TYR* 4.9 5.8 - - + +
45A GLY 5.4 0.4 - - - +
48A PHE* 4.4 11.4 - - + -
49A PHE* 3.8 39.5 - - + -
52A LYS* 4.5 21.2 + - + +
172A SER 3.3 2.7 - - - -
173A SER* 3.6 25.1 - - - +
193A GLY* 3.2 2.1 - - - -
194A ASN* 2.9 43.2 + - + +
196A MET* 3.7 36.8 - - + -
209A ARG* 4.1 11.9 - - + -
210A LEU* 1.3 73.1 - - - +
212A SER* 1.3 63.1 + - - +
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Residues in contact with SER 212 (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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49A PHE* 4.4 2.1 - - - -
171A ALA* 3.0 6.3 - - - +
172A SER* 2.8 40.2 + - - +
174A LEU* 5.9 0.5 - - - +
191A PRO* 4.5 3.3 - - - +
192A HIS 2.8 27.1 + - - -
193A GLY* 3.4 4.8 - - - -
210A LEU* 4.4 7.4 + - - +
211A LEU* 1.3 79.6 + - - +
213A ILE* 1.3 65.3 + - - +
214A TYR* 3.6 29.6 + - - -
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Residues in contact with ILE 213 (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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49A PHE* 5.5 1.8 - - + -
52A LYS* 4.2 17.7 - - - +
53A LEU* 3.9 28.0 - - + -
56A HIS* 3.6 34.3 - - + +
58A ILE* 4.0 12.8 - - + -
170A VAL 3.5 10.3 - - - +
171A ALA* 4.2 0.9 - - + -
211A LEU 6.0 0.2 - - - -
212A SER* 1.3 79.2 - - - +
214A TYR* 1.3 71.0 + - - +
215A THR* 3.7 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