Contacts of the strand formed by residues 2379 - 2385 (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 SER2379 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2372C THR* 3.6 2.0 - - - -
2373C ILE 3.2 1.4 + - - -
2374C SER* 3.2 36.7 + - - -
2377C SER* 2.9 5.0 + - - -
2378C ARG* 1.3 77.2 - - - +
2380C GLY* 1.3 69.4 + - - +
2406C ASN* 3.0 23.4 + - - -
2408C ASN 3.4 12.3 - - - -
2409C TRP* 3.8 5.2 - - - -
2410C SER* 3.5 1.1 + - - -
3478C SIA 3.4 34.3 + - - -
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Residues in contact with GLY2380 (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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2372C THR* 3.3 9.0 - - - -
2373C ILE* 3.6 7.2 - - - -
2379C SER* 1.3 77.2 - - - +
2381C TYR* 1.3 61.8 + - - +
2404C VAL* 3.1 16.4 - - - -
2405C ASN 3.5 13.9 + - - -
2406C ASN* 3.8 5.3 - - - +
2408C ASN 2.8 15.0 + - - -
2410C SER* 2.9 20.3 + - - -
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Residues in contact with TYR2381 (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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2358C GLY* 4.9 0.3 - - - -
2359C PHE* 3.1 19.9 + + - -
2370C GLY* 3.1 22.1 + - - -
2371C ARG* 3.4 33.3 - - - -
2372C THR* 4.0 10.5 - - + -
2373C ILE* 3.5 5.3 - - - +
2380C GLY* 1.3 78.8 - - - +
2382C GLU* 1.3 72.8 + - - +
2383C MET* 4.0 10.3 - - - -
2402C VAL* 3.8 1.6 - - - -
2403C ILE* 2.8 32.0 + - + -
2404C VAL* 2.7 31.9 + - + +
2410C SER* 4.5 2.2 - - - -
2411C GLY 5.0 4.3 - - - -
2413C SER* 2.7 35.6 + - - -
2430C PHE* 4.4 0.7 - + - -
2432C VAL* 3.8 30.3 - - + -
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Residues in contact with GLU2382 (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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2334C ARG* 4.5 0.7 + - - -
2369C LEU 3.8 0.9 - - - +
2370C GLY* 3.5 4.0 - - - -
2371C ARG* 2.9 70.7 + - + +
2372C THR 3.8 5.7 - - - +
2373C ILE* 3.9 23.4 - - + +
2381C TYR* 1.3 78.2 - - - +
2383C MET* 1.3 61.3 + - - +
2384C LEU* 4.0 12.3 - - + -
2401C GLN 3.4 8.5 - - - +
2402C VAL* 4.6 1.1 - - - -
2403C ILE 4.3 0.4 - - - +
3489C MAN 2.6 44.5 + - - +
3G MAN 3.8 6.6 + - - -
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Residues in contact with MET2383 (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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2103C TRP* 3.6 49.8 - - + +
2359C PHE* 3.6 38.4 - - + -
2368C TRP* 3.8 20.4 - - + -
2369C LEU 3.6 9.9 - - - -
2370C GLY* 3.6 11.4 - - - -
2381C TYR* 4.0 4.5 - - - -
2382C GLU* 1.3 72.7 - - - +
2384C LEU* 1.3 61.7 + - - +
2400C ASN* 3.3 5.0 - - - -
2401C GLN* 2.8 36.0 + - + +
2403C ILE* 3.8 8.0 - - + +
2430C PHE* 3.6 25.1 - - + -
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Residues in contact with LEU2384 (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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2328C VAL* 3.7 20.9 - - + -
2368C TRP* 3.3 4.6 - - - -
2369C LEU* 2.8 45.2 + - + +
2371C ARG* 3.7 35.9 - - + +
2382C GLU* 3.8 10.5 - - + +
2383C MET* 1.3 83.8 - - - +
2385C LYS* 1.3 62.5 + - - +
2386C VAL* 3.4 14.3 + - + +
2397C PRO* 4.2 11.2 - - + -
2399C SER 3.7 1.8 - - - +
2400C ASN* 3.7 8.5 - - + -
3488C MAN 6.0 0.2 - - - -
3489C MAN 3.6 23.6 - - - +
3G MAN 3.6 17.0 - - - +
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Residues in contact with LYS2385 (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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2099C GLU* 5.1 2.6 - - - +
2100C VAL 2.9 14.3 + - - +
2101C ASN* 2.9 28.9 + - - +
2365C GLU 3.7 21.3 - - - +
2366C ASN* 4.1 11.9 + - - +
2367C SER 3.4 13.2 - - - +
2368C TRP* 3.5 28.4 - - + +
2384C LEU* 1.3 68.9 - - - +
2386C VAL* 1.3 57.0 + - - +
2387C PRO* 3.5 2.2 - - + +
2397C PRO* 3.2 2.1 - - - +
2398C ILE* 2.8 50.9 + - + -
2399C SER* 3.1 34.4 + - - +
2460C ARG* 6.3 1.3 - - - +
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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