Contacts of the strand formed by residues 2399 - 2409 (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 SER2399 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2101C ASN 4.8 1.4 + - - -
2368C TRP* 3.6 11.9 - - - -
2384C LEU* 3.7 3.1 - - - -
2385C LYS* 3.1 47.0 + - - +
2397C PRO* 4.2 2.8 - - - +
2398C ILE* 1.3 84.1 - - - +
2400C ASN* 1.3 64.2 + - - +
2460C ARG* 5.2 9.6 + - - -
1G NAG 3.3 24.5 - - - -
2G BMA 3.4 8.2 - - - -
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Residues in contact with ASN2400 (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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2368C TRP* 4.8 2.5 - - - -
2383C MET 3.3 7.2 - - - -
2384C LEU* 3.7 5.4 - - + -
2399C SER* 1.3 77.9 + - - +
2401C GLN* 1.3 67.1 + - - +
2402C VAL* 4.4 2.9 + - - +
3489C MAN 3.4 47.3 + - - +
1G NAG 3.3 35.4 + - - +
2G BMA 2.9 31.3 + - - -
3G MAN 3.5 10.3 - - - -
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Residues in contact with GLN2401 (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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2102C SER* 3.6 9.9 + - - -
2103C TRP* 2.8 67.1 + - + +
2368C TRP* 4.9 1.6 - - + -
2382C GLU* 3.4 2.9 - - - -
2383C MET* 2.8 39.0 + - + +
2400C ASN* 1.3 78.6 - - - +
2402C VAL* 1.3 67.0 + - - +
2403C ILE* 3.5 14.3 + - + +
2454C LEU* 4.3 4.8 - - - +
2461C LEU 5.1 1.8 - - - -
2462C GLY 5.1 0.2 + - - -
2463C SER* 3.4 34.5 - - - +
2466C TRP* 5.8 1.0 - - - +
1G NAG 4.2 10.1 - - + +
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Residues in contact with VAL2402 (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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2373C ILE* 4.3 10.8 - - + -
2381C TYR 3.8 4.0 - - - +
2382C GLU* 4.4 1.3 - - - +
2400C ASN* 4.4 3.1 + - - +
2401C GLN* 1.3 77.1 + - - +
2403C ILE* 1.3 65.1 + - - +
2404C VAL 3.6 27.6 - - - +
2405C ASN* 3.7 13.5 - - + +
2463C SER* 4.1 9.7 + - - +
2464C TRP 3.9 13.2 - - - +
2465C SER* 5.0 6.1 - - - +
3489C MAN 3.8 30.7 - - - -
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Residues in contact with ILE2403 (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* 4.7 1.3 - - + -
2381C TYR* 2.8 21.7 + - + +
2383C MET* 3.8 17.5 - - + +
2401C GLN* 3.8 35.4 - - + +
2402C VAL* 1.3 77.0 - - - +
2404C VAL* 1.3 65.3 + - + +
2430C PHE* 3.7 24.9 - - + -
2432C VAL* 4.1 15.7 - - + -
2452C VAL* 4.6 4.7 - - + -
2454C LEU* 3.9 31.9 - - + -
2464C TRP 4.8 0.9 - - - -
2465C SER* 3.5 3.0 - - - -
2466C TRP* 2.8 36.4 + - + -
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Residues in contact with VAL2404 (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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2373C ILE* 3.4 4.7 - - - +
2380C GLY* 3.1 2.8 - - - +
2381C TYR* 2.7 49.9 + - + +
2402C VAL* 3.6 2.7 - - - -
2403C ILE* 1.3 90.7 - - + +
2405C ASN* 1.3 74.0 + - - +
2408C ASN* 3.9 25.8 - - + +
2409C TRP 4.1 11.7 - - - +
2410C SER* 5.0 0.4 - - - -
2432C VAL* 4.3 4.7 - - + -
2434C LEU* 3.8 23.1 - - + -
2452C VAL* 4.8 0.9 - - + -
2465C SER* 3.6 3.6 - - - -
2466C TRP 4.2 7.0 - - - +
2467C HIS* 4.2 12.6 - - + -
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Residues in contact with ASN2405 (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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2373C ILE* 4.4 0.9 - - - -
2380C GLY* 3.5 0.6 - - - -
2402C VAL* 3.7 12.9 - - + +
2404C VAL* 1.3 75.9 - - - +
2406C ASN* 1.3 59.1 + - - +
2407C GLN* 3.1 20.7 + - + +
2408C ASN* 2.8 42.7 + - - +
2465C SER* 3.0 35.2 + - - +
2467C HIS* 4.0 6.5 + - - -
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Residues in contact with ASN2406 (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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2373C ILE* 3.8 30.5 - - + +
2374C SER* 3.7 5.2 + - - +
2379C SER* 3.0 41.6 + - - -
2380C GLY* 3.9 4.0 - - - -
2404C VAL 3.8 0.8 + - - -
2405C ASN* 1.3 71.2 - - - +
2407C GLN* 1.3 56.2 + - - +
2408C ASN 3.3 1.7 + - - -
3478C SIA 2.6 59.0 + - - +
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Residues in contact with GLN2407 (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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2405C ASN* 2.9 18.9 + - + +
2406C ASN* 1.3 80.7 - - - +
2408C ASN* 1.3 67.0 + - - +
2409C TRP* 5.7 0.3 + - - -
3478C SIA 3.8 20.3 - - - +
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Residues in contact with ASN2408 (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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2379C SER* 3.4 2.4 - - - -
2380C GLY* 2.8 31.4 + - - -
2404C VAL* 3.9 6.4 - - + +
2405C ASN* 2.8 29.8 + - - +
2406C ASN 3.3 0.4 - - - -
2407C GLN* 1.3 86.7 + - - +
2409C TRP* 1.3 59.7 + - - +
2436C ARG* 5.6 5.9 - - - +
2467C HIS* 3.3 47.0 + - + +
2468C ASP* 5.2 2.0 - - - +
2469C GLY 5.5 1.8 - - - +
3478C SIA 3.9 6.7 - - - -
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Residues in contact with TRP2409 (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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2377C SER* 4.8 1.8 - - - -
2378C ARG* 3.6 17.0 - - + +
2379C SER* 3.8 6.7 - - - -
2404C VAL* 4.1 3.7 - - - +
2408C ASN* 1.3 79.2 - - - +
2410C SER* 1.3 63.3 - - - +
2434C LEU* 3.8 21.7 - - - +
2435C ILE* 3.4 20.8 - - + +
2436C ARG* 4.4 9.6 - - - -
2440C LYS* 3.7 57.7 - - + -
2441C GLU* 3.6 37.0 + - + +
2468C ASP* 5.4 2.6 + - - +
3478C SIA 3.3 64.0 - - + +
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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