Contacts of the strand formed by residues 363 - 375 (chain C) in PDB entry 1NVP
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 ARG 363 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358C MET 3.7 0.2 - - - +
359C ASN* 3.0 7.9 - - - -
360C LEU 2.9 28.9 + - - +
361C ASN* 3.5 2.0 + - + -
362C GLY* 1.3 78.2 - - - +
364C ASP* 1.3 61.2 + - - +
365C TYR* 3.5 30.0 - - + +
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Residues in contact with ASP 364 (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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10B VAL* 4.4 18.2 - - + +
14B TYR* 2.5 35.7 + - + +
357C ILE* 4.4 6.1 - - - +
358C MET 3.2 6.7 - - - -
359C ASN* 2.5 35.5 + - - +
362C GLY 4.7 0.2 - - - +
363C ARG* 1.3 73.4 - - - +
365C TYR* 1.3 68.3 + - - +
10D THR* 2.7 30.3 + - - -
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Residues in contact with TYR 365 (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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10B VAL* 5.0 3.4 - - - -
357C ILE* 3.4 3.1 - - - +
358C MET* 2.5 60.5 + - + +
360C LEU* 3.8 30.7 + - + -
361C ASN* 5.5 1.0 + - - -
363C ARG* 3.5 39.5 - - + +
364C ASP* 1.3 77.9 - - - +
366C ILE* 1.3 70.1 + - - +
83D GLU* 4.5 14.1 - - - +
88D ILE* 3.4 35.6 - - + +
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Residues in contact with ILE 366 (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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9B THR 5.8 0.4 - - - +
10B VAL* 4.5 21.2 - - + +
13B LEU* 3.6 33.4 - - + -
14B TYR* 4.5 14.1 - - + +
356C GLY 3.2 12.1 - - - +
357C ILE* 4.3 11.7 - - + -
358C MET* 4.8 0.4 - - - +
365C TYR* 1.3 85.9 - - - +
367C PHE* 1.3 70.1 + - - +
48D LEU* 3.6 15.7 - - + -
52D VAL* 3.3 35.6 - - + +
54D ASN* 3.2 21.2 + - - +
56D VAL* 4.6 2.3 - - - +
83D GLU* 4.4 2.3 - - - +
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Residues in contact with PHE 367 (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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335C VAL* 4.0 9.6 - - + -
337C CYS* 3.9 12.6 - - + -
353C LEU* 4.2 6.1 - - + -
354C LYS* 3.4 21.8 - - - -
355C ASP* 3.3 3.5 - - - -
356C GLY* 2.9 49.6 + - - +
358C MET* 3.3 40.8 - - + -
366C ILE* 1.3 84.5 - - - +
368C SER* 1.3 59.3 + - - +
369C LYS 3.5 22.7 - - - +
370C ALA* 3.5 24.9 - - + -
48D LEU* 5.3 0.3 - - - +
52D VAL* 4.3 1.9 - - - +
54D ASN* 3.9 7.9 - - - +
56D VAL* 3.4 20.6 - - + -
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Residues in contact with SER 368 (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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354C LYS* 3.0 25.8 - - - +
355C ASP* 3.1 15.7 + - - +
367C PHE* 1.3 75.1 - - - +
369C LYS* 1.3 67.6 + - - +
48D LEU 5.6 0.4 - - - -
52D VAL* 4.0 10.1 - - - +
53D ARG* 3.2 24.6 + - - -
54D ASN* 2.6 32.5 + - - -
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Residues in contact with LYS 369 (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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340C ASP* 5.2 6.7 - - - +
352C HIS* 6.4 2.7 - - - +
353C LEU 3.2 11.7 - - - +
354C LYS* 4.6 4.5 - - + -
367C PHE* 3.3 6.6 - - - +
368C SER* 1.3 94.0 + - - +
370C ALA* 1.3 60.3 + - - +
371C ILE* 4.0 28.7 - - - +
54D ASN 3.4 1.3 + - - +
55D ARG* 3.4 29.3 - - + +
56D VAL 2.8 25.3 + - - -
16F C 5.7 2.8 + - - -
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Residues in contact with ALA 370 (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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351C PHE 3.6 1.4 - - - +
352C HIS 3.7 0.5 - - - -
353C LEU* 2.7 46.4 + - + +
367C PHE* 3.5 35.7 - - + -
369C LYS* 1.3 75.8 - - - +
371C ILE* 1.3 63.9 + - - +
372C GLY 4.2 0.4 - - - -
56D VAL* 3.3 13.2 - - + +
58D PHE* 4.4 15.5 - - + -
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Residues in contact with ILE 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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350C LYS* 6.4 0.7 - - + -
351C PHE 3.3 8.7 - - - +
352C HIS* 4.8 25.4 - - + +
369C LYS* 4.0 20.9 - - - +
370C ALA* 1.3 78.1 - - - +
372C GLY* 1.3 66.5 + - - +
373C ASP* 5.5 4.7 - - - +
55D ARG* 3.5 35.0 - - - +
56D VAL 3.0 6.9 + - - -
57D ASN* 3.1 18.1 - - - +
58D PHE* 2.9 23.5 + - - +
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Residues in contact with GLY 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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350C LYS* 3.4 1.4 - - - +
351C PHE* 3.0 36.3 + - - +
371C ILE* 1.3 78.6 - - - +
373C ASP* 1.3 72.1 + - - +
58D PHE* 2.8 32.4 - - - -
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Residues in contact with ASP 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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349C TRP 3.6 3.7 - - - +
350C LYS* 3.2 30.6 - - - +
351C PHE* 4.2 1.7 - - - -
371C ILE* 5.5 5.5 - - - +
372C GLY* 1.3 81.7 - - - +
374C ALA* 1.3 62.4 + - - +
58D PHE* 2.8 7.7 + - - +
59D ARG* 3.2 40.4 + - + +
60D GLY 2.9 24.9 + - - +
76D LEU* 5.0 0.7 - - - +
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Residues in contact with ALA 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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347C ASN 3.8 0.3 - - - +
348C LYS* 3.9 1.7 - - - +
349C TRP* 2.9 35.7 + - - +
351C PHE* 3.9 11.2 - - + -
373C ASP* 1.3 76.5 - - - +
375C GLU* 1.3 62.9 + - - +
60D GLY 2.9 18.4 - - - +
62D LEU* 3.6 12.6 - - + +
76D LEU* 3.3 29.2 - - + -
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Residues in contact with GLU 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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347C ASN* 3.3 13.8 + - - +
348C LYS* 2.7 40.7 + - + +
374C ALA* 1.3 75.1 - - - +
376C TRP* 1.3 58.6 + - - +
60D GLY 3.5 5.3 + - - -
61D SER* 3.5 10.0 - - - -
62D LEU* 2.7 24.6 + - - +
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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