Contacts of the strand formed by residues 334 - 345 (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 VAL 334 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332C GLU* 3.1 42.3 + - + +
333C ASN* 1.3 78.6 - - - +
335C VAL* 1.3 72.0 + - - +
336C VAL* 3.8 24.2 - - + -
357C ILE 3.9 1.3 - - - +
358C MET* 3.4 3.3 - - - -
359C ASN* 3.1 32.5 + - + +
360C LEU* 4.7 0.7 - - - +
8D ASN* 5.1 15.9 - - - +
93D VAL* 4.4 0.4 - - - +
94D LYS* 3.3 20.2 - - + +
96D VAL* 5.3 4.0 - - + -
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Residues in contact with VAL 335 (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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334C VAL* 1.3 81.1 - - - +
336C VAL* 1.3 67.3 + - - +
337C CYS* 4.1 17.5 - - - -
353C LEU* 5.2 2.0 - - + -
357C ILE 3.7 3.8 - - - +
358C MET* 3.6 27.1 - - + -
360C LEU* 4.7 1.1 - - + -
367C PHE* 4.0 25.6 - - + -
81D PHE* 4.4 7.2 - - + -
93D VAL* 4.0 18.8 - - + -
94D LYS 2.9 5.9 + - - +
95D ILE* 3.4 21.4 - - + -
96D VAL 2.9 26.9 + - - +
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Residues in contact with VAL 336 (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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334C VAL* 3.8 17.0 - - + -
335C VAL* 1.3 77.7 - - - +
337C CYS* 1.3 60.5 + - - +
356C GLY* 3.3 1.6 - - - -
357C ILE 3.1 32.4 + - - +
5D LEU* 2.9 56.3 - - + +
6D TYR* 3.8 9.3 - - + +
8D ASN* 4.2 18.8 - - + +
9D THR* 4.6 10.3 - - + -
96D VAL* 3.5 12.3 - - + +
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Residues in contact with CYS 337 (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* 4.1 10.5 - - + -
336C VAL* 1.3 78.1 - - - +
338C GLN* 1.3 67.0 - - - +
353C LEU* 3.9 26.7 - - - -
354C LYS 3.2 14.6 - - - +
355C ASP 3.6 7.6 - - - -
356C GLY* 3.6 10.1 - - - -
367C PHE* 3.9 4.3 - - + -
5D LEU* 3.1 17.6 - - - +
95D ILE* 4.2 2.5 - - - -
96D VAL 3.0 10.5 + - - +
97D ALA* 3.1 21.7 - - - -
98D CYS 3.0 18.9 + - - -
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Residues in contact with GLN 338 (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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337C CYS* 1.3 78.9 - - - +
339C TYR* 1.3 58.7 + - - +
353C LEU* 3.6 3.1 - - - -
354C LYS* 3.0 54.2 + - + +
355C ASP* 4.0 18.2 + - - +
3D TYR* 4.4 16.7 - - + -
5D LEU* 3.6 11.6 - - + +
6D TYR* 2.6 27.3 + - - +
45D ASN* 3.9 12.9 + - - +
97D ALA* 4.2 3.1 - - - -
98D CYS* 2.8 21.3 - - + +
99D ASP 4.2 11.4 - - - +
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Residues in contact with TYR 339 (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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338C GLN* 1.3 74.7 - - - +
340C ASP* 1.3 71.3 + - - +
341C LYS* 4.6 1.6 - - - +
342C ILE* 3.9 20.4 - - + -
352C HIS 3.8 3.1 - - - -
353C LEU* 3.8 18.8 - - + -
354C LYS* 5.0 2.9 - - - -
67D PHE* 3.6 12.6 - - - -
70D ASN* 2.8 26.5 + - - +
72D TRP* 3.6 26.7 - + - -
97D ALA* 3.3 24.7 - - + -
98D CYS 2.7 24.2 + - - -
99D ASP* 3.2 60.1 - - - +
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Residues in contact with ASP 340 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338C GLN 4.2 0.2 + - - -
339C TYR* 1.3 81.6 - - - +
341C LYS* 1.3 73.6 + - + +
352C HIS* 2.8 24.8 + - + +
353C LEU 4.5 2.9 - - - +
354C LYS* 3.3 47.8 + - - +
369C LYS* 5.2 7.8 - - - +
99D ASP* 5.0 1.7 - - - +
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Residues in contact with LYS 341 (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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339C TYR* 5.0 1.3 - - - -
340C ASP* 1.3 89.9 - - + +
342C ILE* 1.3 69.7 + - - +
343C HIS* 4.1 2.7 - - + -
350C LYS 4.1 1.4 - - - +
351C PHE 3.9 0.2 - - - -
352C HIS* 2.9 45.9 + - + +
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Residues in contact with ILE 342 (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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339C TYR* 3.9 25.9 - - + -
341C LYS* 1.3 83.5 - - - +
343C HIS* 1.3 62.6 + - - +
349C TRP* 3.9 30.7 - - + -
350C LYS 3.7 4.9 - - - +
351C PHE* 4.2 9.9 - - + -
353C LEU* 4.1 11.9 - - + -
72D TRP* 3.6 38.5 - - + +
74D PHE* 3.9 30.5 - - + -
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Residues in contact with HIS 343 (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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341C LYS* 5.5 2.7 - - + -
342C ILE* 1.3 76.6 - - - +
344C ARG* 1.3 77.6 + - - +
345C SER* 3.2 21.4 + - - -
348C LYS 5.0 1.6 - - - -
349C TRP* 3.2 9.3 - - - +
350C LYS* 2.8 56.4 + - + +
352C HIS* 6.2 1.6 - - + +
6E G 3.4 36.0 + - - -
7E G 3.7 26.9 + - - -
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Residues in contact with ARG 344 (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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191A GLU* 5.4 1.4 + - - -
203A ARG* 2.9 35.6 - - - +
343C HIS* 1.3 88.5 + - - +
345C SER* 1.3 68.3 + - - +
346C LYS* 2.8 51.7 + - - +
348C LYS 3.2 9.9 - - - +
349C TRP* 3.6 46.5 - - + +
4F T 4.3 9.5 + - - -
5F T 2.9 32.9 + - - -
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Residues in contact with SER 345 (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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343C HIS* 3.2 23.3 + - - -
344C ARG* 1.3 71.7 + - - +
346C LYS* 1.3 76.4 + - - +
348C LYS* 2.7 35.0 + - - +
6E G 4.5 9.9 + - - -
7E G 5.2 1.4 + - - -
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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