Contacts of the strand formed by residues 370 - 376 (chain C) in PDB entry 1DVM
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 VAL 370 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C SER* 3.0 20.3 + - - -
17C VAL* 3.6 21.1 - - + -
36C PRO* 3.3 31.3 - - + +
37C TYR* 3.4 18.0 + - - +
256C ALA* 4.9 6.5 - - - +
259C ILE* 4.7 15.5 - - + -
361C VAL* 4.3 23.1 - - + -
362C VAL 3.8 4.7 - - - -
363C ARG* 4.1 7.4 - - + +
368C GLY 3.9 10.8 - - - +
369C THR* 1.3 67.5 - - - +
371C LEU* 1.3 63.8 + - - +
372C PHE 3.5 3.4 - - - +
373C MET* 4.8 3.1 - - - -
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Residues in contact with LEU 371 (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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35C SER* 2.7 32.8 + - - -
37C TYR* 3.8 30.4 + - + -
82C LEU* 4.0 30.1 - - + -
87C ASN* 5.4 1.6 - - - +
91C ILE* 5.3 11.9 - - + -
169C LEU* 4.7 2.0 - - + +
171C PHE* 6.4 0.2 - - + -
233C LEU* 3.6 33.4 - - + -
362C VAL* 2.9 13.4 + - + +
364C HIS* 4.2 16.4 - - + +
369C THR* 3.0 13.5 + - + +
370C VAL* 1.3 74.1 - - - +
372C PHE* 1.3 79.1 + - + +
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Residues in contact with PHE 372 (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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33C VAL* 5.0 2.0 - - + -
34C PHE 3.2 6.3 - - - +
35C SER* 3.9 3.4 - - - +
36C PRO* 4.1 2.0 - - - -
91C ILE* 3.4 32.5 - - + -
169C LEU* 3.4 41.1 - - + -
170C TYR 4.2 1.3 - - - -
171C PHE* 3.5 33.2 - + + -
324C VAL* 3.5 24.7 - - + -
325C LYS 5.3 0.2 - - - -
326C ILE* 4.9 9.4 - - + -
360C PHE* 4.7 3.4 - - + -
361C VAL* 3.6 5.0 - - - +
362C VAL* 3.0 52.3 + - + +
370C VAL* 4.6 1.3 - - - +
371C LEU* 1.3 93.4 + - + +
373C MET* 1.3 65.3 + - - +
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Residues in contact with MET 373 (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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17C VAL* 3.9 30.1 - - + +
20C PHE* 3.0 40.2 - - + -
33C VAL* 3.4 1.7 - - - +
34C PHE* 2.5 41.4 + - - +
36C PRO* 3.9 24.0 - - + -
254C LEU* 3.3 32.8 - - + -
259C ILE* 6.0 2.9 - - - -
359C LEU* 5.7 2.0 - - + -
360C PHE* 3.5 11.7 - - - +
361C VAL* 3.9 25.4 - - + -
370C VAL* 4.8 3.8 - - + -
372C PHE* 1.3 75.4 - - - +
374C GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 374 (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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20C PHE* 3.5 17.7 - - - -
32C VAL 3.2 12.3 - - - -
359C LEU* 3.2 8.1 - - - +
360C PHE* 3.0 40.7 + - - -
373C MET* 1.3 80.5 - - - +
375C GLN* 1.3 60.8 + - - -
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Residues in contact with GLN 375 (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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20C PHE* 4.7 1.5 - - + -
24C ALA* 4.0 26.6 + - - +
27C SER* 3.5 14.9 + - - -
28C LYS 3.9 6.2 - - - +
30C ARG 3.3 23.3 - - - +
31C ASN* 3.5 1.7 - - - -
32C VAL* 2.9 38.7 + - + +
247C LEU* 3.9 13.6 - - + +
251C THR* 4.7 10.1 - - - +
280C LEU* 4.0 1.2 - - - +
358C PHE 3.2 8.3 - - - +
359C LEU* 3.8 18.1 - - + +
360C PHE* 4.3 0.4 - - - -
374C GLY* 1.3 74.1 - - - -
376C VAL* 1.3 62.0 + - - +
377C MET* 4.2 12.2 - - - +
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Residues in contact with VAL 376 (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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31C ASN* 4.0 13.9 - - - +
189C PHE* 3.9 1.3 - - + -
278C PHE* 4.4 8.7 - - + -
280C LEU* 4.3 9.2 - - + -
357C PRO* 3.1 22.2 - - - +
358C PHE* 2.8 60.5 + - + +
360C PHE* 3.8 15.0 - - + -
375C GLN* 1.3 73.9 - - - +
377C MET* 1.3 61.5 + - - +
378C GLU 4.1 8.7 - - - +
379C PRO* 4.1 24.5 - - + -
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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