Contacts of the strand formed by residues 51 - 54 (chain 1) in PDB entry 1K2I
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 TRP 51 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461 LEU* 3.7 1.1 - - - -
471 ILE* 3.2 39.0 + - + -
481 ASN* 2.7 39.1 + - - +
501 ASN* 1.3 81.5 - - + +
521 VAL* 1.3 67.4 + - - +
891 PHE* 3.7 39.0 - + - -
1051 LEU* 4.0 17.3 - - + -
1061 LEU 3.3 18.2 - - - -
1071 LYS* 3.2 35.0 - - + +
1081 LEU* 4.5 0.6 - - - +
2411 THR* 4.2 11.7 - - + -
2421 LEU* 3.6 31.3 + - + +
2451 ASN* 3.5 30.8 + - + -
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Residues in contact with VAL 52 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311 VAL* 3.9 21.5 - - + -
331 LEU* 5.1 0.7 - - + -
441 GLY* 4.3 2.7 - - - -
451 SER 3.4 8.7 - - - +
461 LEU* 3.6 24.9 - - + -
511 TRP* 1.3 76.7 - - - +
531 VAL* 1.3 76.7 + - - +
541 THR* 5.0 1.1 - - - -
661 VAL* 4.1 13.0 - - + -
1041 THR 3.9 0.3 - - - +
1051 LEU* 3.5 4.2 - - - +
1061 LEU* 2.8 57.0 + - + +
1081 LEU* 4.1 21.8 - - + -
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Residues in contact with VAL 53 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441 GLY* 3.4 3.5 - - - -
451 SER* 2.8 49.8 + - - +
471 ILE* 3.6 25.6 - - + -
521 VAL* 1.3 73.4 - - - +
541 THR* 1.3 60.5 + - - +
1031 ILE* 5.0 5.2 - - + -
1041 THR 3.6 4.0 - - - +
1051 LEU* 3.2 26.5 - - + -
1231 LEU* 5.3 2.5 - - + -
1961 GLY 3.8 1.9 - - - +
2091 LEU* 3.7 29.6 - - + -
2121 ILE* 4.9 12.3 - - + -
2381 VAL* 5.0 8.7 - - + -
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Residues in contact with THR 54 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 LEU* 3.5 21.8 - - + +
431 GLY 2.9 23.5 + - - -
441 GLY* 4.3 2.0 - - - -
521 VAL* 5.0 0.4 - - - -
531 VAL* 1.3 75.5 - - - +
551 ALA* 1.3 74.6 + - - +
581 CYS* 3.9 4.9 - - - -
601 VAL* 4.4 5.6 - - + -
1031 ILE* 3.5 10.0 - - - +
1041 THR* 2.9 46.2 + - + +
1061 LEU* 4.2 14.1 - - + -
1961 GLY* 3.4 10.6 - - - -
2121 ILE* 4.0 9.4 - - - +
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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
------------------------------------------------------------
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