Contacts of the strand formed by residues 2268 - 2274 (chain C) in PDB entry 1W21
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 LYS2268 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2219C ILE* 3.8 20.6 - - + -
2220C THR* 3.8 5.2 - - - +
2264C PHE* 3.3 4.1 - - - -
2265C LYS 3.0 34.0 + - - +
2266C GLU* 4.0 8.3 - - + +
2267C GLY* 1.3 79.2 - - - +
2269C ILE* 1.3 62.2 + - - +
2270C GLN* 3.0 15.8 + - - +
3422D ASN* 5.1 15.0 + - - -
3424D GLU* 5.3 6.5 + - - -
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Residues in contact with ILE2269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2220C THR* 4.1 15.2 + - + +
2222C ILE* 4.0 28.9 - - + -
2262C ILE* 3.8 7.0 - - + -
2263C TYR 3.8 3.6 - - - -
2264C PHE* 3.6 21.5 - - + -
2267C GLY 4.1 0.4 + - - -
2268C LYS* 1.3 72.5 - - - +
2270C GLN* 1.4 64.8 + - - +
2271C LYS* 3.7 15.5 - - - +
2272C ILE* 3.7 35.0 - - + -
3459D LYS* 5.2 5.8 - - - +
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Residues in contact with GLN2270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2243C VAL* 5.2 5.6 - - + -
2263C TYR* 2.8 19.9 + - + +
2264C PHE 4.1 1.6 - - - -
2265C LYS* 3.7 38.8 - - + +
2268C LYS* 3.0 26.3 - - - +
2269C ILE* 1.4 78.5 - - - +
2271C LYS* 1.3 60.6 + - - +
2317C MET* 4.1 25.0 - - + +
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Residues in contact with LYS2271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2263C TYR* 2.9 38.4 + - + +
2269C ILE* 3.6 4.6 - - - +
2270C GLN* 1.3 82.6 - - - +
2272C ILE* 1.3 75.8 + - - +
2273C GLU* 3.7 21.9 + - + -
2316C MET 3.9 7.5 + - - -
2317C MET* 2.8 52.6 + - + +
2318C THR* 4.1 6.5 - - - +
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Residues in contact with ILE2272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2222C ILE* 6.6 0.2 - - + -
2260C LYS* 4.1 30.7 - - + +
2261C ILE 3.7 3.6 - - - -
2262C ILE* 4.1 23.6 - - + -
2269C ILE* 3.7 30.5 - - + -
2271C LYS* 1.3 83.3 - - - +
2273C GLU* 1.3 68.9 + - - +
2274C GLU* 6.2 0.4 - - + -
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Residues in contact with GLU2273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2260C LYS* 3.2 6.5 - - - +
2261C ILE* 2.8 38.6 + - + +
2263C TYR* 2.7 29.3 + - + -
2271C LYS* 3.7 25.7 + - - -
2272C ILE* 1.3 76.9 - - - +
2274C GLU* 1.3 67.8 + - - +
2317C MET 3.3 17.5 - - - +
2318C THR* 3.4 14.1 - - - +
2319C HIS* 2.7 28.8 + - + +
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Residues in contact with GLU2274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259C THR 3.8 5.8 - - - +
2260C LYS* 4.5 20.4 - - + -
2272C ILE* 4.5 1.1 + - + -
2273C GLU* 1.3 74.8 - - - +
2275C LEU* 1.3 69.1 + - - +
2276C ALA* 3.3 2.9 + - - +
2319C HIS* 3.2 16.7 - - - -
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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