Contacts of the strand formed by residues 95 - 102 (chain 2) 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 VAL 95 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232 VAL* 3.4 23.1 - - + +
252 SER* 4.9 6.7 - - - +
662 THR* 3.7 17.5 - - - +
672 ASP 4.5 3.3 + - - -
712 GLN* 4.2 9.4 + - - +
762 TYR* 3.6 46.1 - - + +
932 ALA 3.9 0.4 + - - +
942 PRO* 1.3 74.3 - - - +
962 LEU* 1.3 69.0 + - - +
972 VAL* 4.1 3.2 + - + +
553 LEU* 5.0 2.9 - - + -
1073 MET* 3.9 25.6 - - + -
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Residues in contact with LEU 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 ALA* 4.0 20.2 - - + -
232 VAL 2.7 29.4 + - - +
242 GLY* 3.5 0.5 - - - -
252 SER* 3.1 19.6 + - - -
402 LEU* 4.4 4.0 - - + -
512 PHE* 3.7 39.7 - - + +
522 VAL 4.1 0.9 - - - +
532 LEU* 4.0 24.2 - - + +
642 GLY* 3.9 15.0 - - - +
652 TYR 3.2 13.5 - - - +
662 THR* 4.1 4.0 - - + -
942 PRO* 4.0 13.7 - - + +
952 VAL* 1.3 77.2 - - - +
972 VAL* 1.3 59.8 + - - +
982 SER* 2.9 20.0 + - - +
1103 LEU* 5.8 0.7 - - + -
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Residues in contact with VAL 97 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 SER* 4.2 12.1 - - - +
642 GLY* 3.2 1.7 - - - -
652 TYR* 2.7 62.0 + - + +
672 ASP* 4.9 17.0 - - + +
952 VAL* 4.1 3.3 + - + +
962 LEU* 1.3 70.3 - - - +
982 SER* 1.3 64.0 + - - +
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Residues in contact with SER 98 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 GLY* 3.7 12.5 - - - -
252 SER 3.2 20.0 + - - +
262 PHE* 3.3 37.7 - - - +
532 LEU* 4.7 3.2 - - - +
632 GLU 3.1 14.6 - - - -
642 GLY* 3.9 4.2 - - - -
962 LEU* 2.9 22.3 + - - +
972 VAL* 1.3 77.9 - - - +
992 LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 99 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262 PHE* 3.6 6.4 - - - -
272 PHE* 6.6 0.2 - - - -
622 TYR* 3.6 4.5 - - - -
632 GLU* 2.9 58.2 + - + +
982 SER* 1.3 75.6 - - - +
1002 VAL* 1.3 65.8 + - - +
1012 VAL* 4.0 19.6 - - + +
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Residues in contact with VAL 100 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 PHE* 3.7 8.1 - - + -
272 PHE* 4.1 18.7 - - + -
302 PHE* 3.4 34.5 - - + -
602 LEU* 4.1 25.1 - - + -
612 GLU 3.6 5.8 - - - +
622 TYR* 3.6 23.1 - - + +
992 LYS* 1.3 78.4 - - - +
1012 VAL* 1.3 64.9 + - - +
1022 SER 4.2 0.9 + - - -
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Residues in contact with VAL 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602 LEU* 3.5 7.5 - - - +
612 GLU* 2.8 44.9 + - + +
632 GLU* 4.2 11.4 - - - +
992 LYS* 4.0 32.8 - - + +
1002 VAL* 1.3 77.9 - - - +
1022 SER* 1.3 73.0 + - - +
1032 LYS 3.5 0.3 + - - -
1062 LYS* 4.0 28.9 - - + -
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Residues in contact with SER 102 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592 ARG 4.6 1.2 + - - -
602 LEU* 3.8 15.9 - - - +
1002 VAL 4.2 1.2 + - - -
1012 VAL* 1.3 75.9 - - - +
1032 LYS* 1.3 58.2 + - - +
1042 SER* 3.2 25.3 + - - -
1052 SER* 3.4 15.4 + - - -
1062 LYS* 2.9 30.7 + - - +
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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