Contacts of the strand formed by residues 2368 - 2371 (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 TRP2368 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2100C VAL* 2.8 40.7 + - + +
2101C ASN 3.6 24.0 - - - -
2102C SER* 4.1 1.1 - - - -
2103C TRP* 3.2 53.6 - + + -
2360C ALA* 3.3 4.3 - - - +
2361C PHE* 2.9 40.4 + - + +
2366C ASN 4.5 7.6 - - - -
2367C SER* 1.3 81.3 - - - +
2369C LEU* 1.3 61.6 - - - +
2383C MET* 3.8 28.4 - - + +
2384C LEU 3.3 8.1 - - - -
2385C LYS* 3.5 41.2 - - + +
2399C SER* 3.6 17.9 - - - -
2400C ASN* 4.8 3.4 - - - -
2401C GLN* 4.9 1.8 - - + -
1G NAG 5.0 5.8 - - + -
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Residues in contact with LEU2369 (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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2324C LEU* 4.0 13.9 - - + -
2326C SER* 4.3 4.5 - - - -
2328C VAL* 3.7 36.3 - - + +
2330C THR* 3.8 20.0 - - + +
2360C ALA* 3.6 25.8 - - + -
2362C LEU* 4.0 6.3 - - + -
2368C TRP* 1.3 77.9 - - - +
2370C GLY* 1.3 61.5 + - - +
2382C GLU 3.8 0.9 - - - +
2383C MET* 3.6 3.7 - - - -
2384C LEU* 2.8 39.8 + - + +
2386C VAL* 4.0 18.6 - - + -
2389C ALA* 3.8 26.9 - - + -
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Residues in contact with GLY2370 (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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2307C ARG* 4.9 2.1 + - - -
2330C THR* 3.4 17.0 - - - +
2358C GLY* 5.9 0.3 - - - -
2359C PHE* 3.5 19.5 + - - +
2368C TRP 4.3 0.2 + - - -
2369C LEU* 1.3 73.0 - - - +
2371C ARG* 1.3 65.1 + - - +
2381C TYR* 3.1 20.4 + - - -
2382C GLU 3.5 7.6 - - - -
2383C MET* 3.6 15.9 - - - +
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Residues in contact with ARG2371 (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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2307C ARG* 6.1 0.2 - - - +
2328C VAL* 3.5 11.4 - - - +
2329C LEU 2.8 35.6 + - - -
2330C THR* 3.6 27.6 - - + +
2334C ARG* 3.6 21.9 - - - +
2337C ASP* 3.0 26.6 + - - -
2370C GLY* 1.3 76.4 - - - +
2372C THR* 1.3 68.0 + - - +
2381C TYR* 3.3 16.1 + - - -
2382C GLU* 2.9 57.7 + - + +
2384C LEU* 3.7 16.8 - - + +
3488C MAN 3.1 29.7 + - - -
3G MAN 5.0 2.6 + - - -
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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