Contacts of the strand formed by residues 107 - 112 (chain 3) in PDB entry 4C2M
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 107 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232 VAL* 3.9 18.8 - - + -
242 GLY 3.6 2.0 - - - -
252 SER* 4.2 14.1 - - - -
762 TYR* 5.5 5.2 - - + -
952 VAL* 3.9 26.5 - - + -
553 LEU* 3.5 32.8 - - + -
963 GLU* 2.8 34.0 + - + +
1053 SER* 4.1 11.4 - - - -
1063 ASN* 1.3 84.5 - - + +
1083 THR* 1.3 67.1 - - - +
1313 LEU 4.4 7.1 - - - +
1323 GLN* 5.1 1.6 - - - +
1333 PHE* 4.0 13.0 - - + -
1363 VAL* 5.9 0.2 - - - -
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Residues in contact with THR 108 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232 VAL* 3.9 2.9 - - - +
242 GLY* 2.9 38.1 + - - -
262 PHE* 3.6 22.0 + - - -
272 PHE 5.6 1.3 - - - +
302 PHE* 3.6 36.8 - - + +
1053 SER* 5.7 2.2 - - - +
1063 ASN 5.2 1.1 + - - +
1073 MET* 1.3 80.1 - - - +
1093 LEU* 1.3 65.4 + - - +
1103 LEU* 3.8 6.5 + - - +
1213 ILE* 5.1 5.8 - - + -
1303 PRO* 4.2 18.8 - - + -
1313 LEU 4.7 4.0 - - - +
1333 PHE* 5.4 0.9 - - - -
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Residues in contact with LEU 109 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212 VAL* 4.2 20.6 - - + -
222 ALA 3.6 12.1 - - - +
232 VAL* 4.1 14.8 - - + +
782 VAL* 4.3 7.0 - - + -
383 PHE* 4.2 17.3 - - + -
533 VAL* 4.0 16.6 - - + -
1083 THR* 1.3 72.3 - - - +
1103 LEU* 1.3 72.6 + - - +
1113 VAL* 4.2 3.4 - - + -
1213 ILE* 3.6 3.5 - - - +
1223 ALA* 2.8 40.4 + - + +
1313 LEU* 3.6 39.4 + - + +
1333 PHE* 4.5 12.9 - - + -
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Residues in contact with LEU 110 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212 VAL* 3.3 7.3 - - - +
222 ALA* 2.9 49.8 + - + +
232 VAL 5.5 0.2 - - - -
242 GLY* 4.9 7.6 - - - +
262 PHE* 5.3 8.5 - - + -
382 PHE* 4.1 24.7 - - + -
532 LEU* 4.0 28.9 - - + -
962 LEU* 5.8 0.2 - - + -
1083 THR* 4.3 12.8 - - - +
1093 LEU* 1.3 84.5 - - - +
1113 VAL* 1.3 62.0 + - - +
1193 LEU* 3.8 16.8 - - + +
1203 LYS 3.3 5.6 - - - +
1213 ILE* 3.6 32.1 - - + +
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Residues in contact with VAL 111 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212 VAL* 3.9 4.7 - - + -
383 PHE* 3.5 35.7 - - + -
403 LEU* 4.6 5.6 - - + -
1093 LEU* 4.2 4.0 - - + -
1103 LEU* 1.3 76.3 - - - +
1123 PRO* 1.3 75.5 - - + +
1193 LEU* 3.2 5.3 - - - -
1203 LYS* 2.7 51.2 + - + +
1213 ILE 5.0 0.4 - - - +
1223 ALA* 3.6 31.0 - - + -
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Residues in contact with PRO 112 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202 SER 3.5 17.3 - - - +
212 VAL* 3.8 9.4 - - + -
353 LEU* 4.0 24.9 - - + +
363 LYS 3.6 19.7 - - - +
373 ASN* 5.1 1.1 - - - -
383 PHE* 4.3 11.9 - - + +
1113 VAL* 1.3 96.4 - - + +
1133 SER* 1.3 65.7 + - - +
1143 GLU* 5.3 1.6 - - - +
1163 LYS* 4.7 8.1 - - + -
1183 SER 3.3 8.1 - - - +
1193 LEU* 3.6 3.1 - - + -
1203 LYS* 5.4 0.2 - - - +
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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