Contacts of the strand formed by residues 348 - 360 (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 LYS 348 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343C HIS* 3.8 2.3 - - - +
344C ARG* 3.2 4.7 - - - -
345C SER* 2.7 49.5 + - - +
346C LYS* 3.3 3.3 + - + -
347C ASN* 1.3 89.3 + - - +
349C TRP* 1.3 63.5 + - - +
350C LYS* 5.4 5.5 - - + +
374C ALA 3.9 2.5 - - - +
375C GLU* 2.7 47.6 + - + +
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Residues in contact with TRP 349 (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* 4.7 5.6 - - - -
203A ARG* 4.6 0.2 - - - -
342C ILE* 3.9 21.8 - - + -
343C HIS 3.2 9.6 - - - -
344C ARG* 3.6 35.8 - - + +
347C ASN* 3.9 14.3 + - - +
348C LYS* 1.3 79.9 - - - +
350C LYS* 1.3 65.3 + - - +
351C PHE* 3.8 17.7 - + + -
373C ASP* 3.6 4.9 - - - +
374C ALA 2.9 34.7 + - - +
376C TRP* 3.8 15.1 - - + +
62D LEU* 3.6 21.9 - - + +
65D TYR* 3.4 36.3 - + - -
72D TRP* 3.6 40.4 - + - -
74D PHE* 4.1 11.4 - + - -
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Residues in contact with LYS 350 (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 4.1 1.0 - - - +
342C ILE* 3.7 3.6 - - - +
343C HIS* 2.8 50.5 + - + +
348C LYS* 5.4 6.5 - - + +
349C TRP* 1.3 76.5 - - - +
351C PHE* 1.3 62.6 + - - +
352C HIS* 4.4 17.2 - - + +
371C ILE* 6.4 0.2 - - + -
372C GLY 3.4 4.9 - - - +
373C ASP* 3.2 21.1 - - - +
5E G 3.6 28.9 + - - -
6E G 3.9 14.3 + - - +
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Residues in contact with PHE 351 (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 4.1 2.0 - - - -
342C ILE* 4.2 6.5 - - + -
349C TRP* 3.8 30.3 - + + -
350C LYS* 1.3 74.9 - - - +
352C HIS* 1.3 68.4 + - - +
353C LEU* 3.8 13.5 - - + -
370C ALA 3.6 0.3 - - - +
371C ILE* 3.3 7.8 - - - +
372C GLY 3.0 39.7 + - - +
373C ASP 4.3 1.1 - - - -
374C ALA* 3.9 29.4 - - + -
58D PHE* 3.9 26.7 - + + -
62D LEU* 4.3 13.0 - - + -
74D PHE* 3.5 53.6 - + + -
76D LEU* 4.6 5.8 - - + -
95D ILE* 5.8 0.2 - - + -
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Residues in contact with HIS 352 (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 3.7 0.7 - - - -
340C ASP* 2.8 40.5 + - + +
341C LYS* 2.9 39.1 + - + +
343C HIS* 6.2 1.5 - - + +
350C LYS* 4.4 18.0 - - + +
351C PHE* 1.3 85.7 - - - +
353C LEU* 1.3 60.2 + - - +
369C LYS* 6.4 1.8 - - - +
370C ALA 3.8 2.7 - - - -
371C ILE* 4.8 24.8 - - + +
16F C 5.9 2.7 - - - -
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Residues in contact with LEU 353 (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* 5.2 1.8 - - + -
337C CYS* 3.9 24.7 - - - -
338C GLN 3.6 6.1 - - - +
339C TYR* 3.8 23.1 - - + -
340C ASP* 4.5 2.6 - - - +
342C ILE* 4.1 13.7 - - + -
351C PHE* 4.1 10.8 - - + -
352C HIS* 1.3 81.9 - - - +
354C LYS* 1.3 61.7 + - - +
367C PHE* 4.0 3.4 - - + -
369C LYS* 3.2 9.9 - - - +
370C ALA* 2.7 49.3 + - + +
58D PHE* 3.9 28.9 - - + -
74D PHE* 5.4 1.1 - - + -
95D ILE* 4.2 16.4 - - + -
97D ALA* 4.4 5.2 - - + -
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Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C CYS* 3.2 3.3 - - - +
338C GLN* 3.0 57.2 + - + +
339C TYR 5.0 4.2 + - - -
340C ASP* 3.3 34.4 + - - +
353C LEU* 1.3 75.9 - - - +
355C ASP* 1.3 82.8 + - - +
356C GLY 3.4 2.7 - - - -
367C PHE* 3.4 4.9 - - - -
368C SER 3.0 18.8 - - - +
369C LYS* 4.5 3.6 - - + -
99D ASP 5.8 3.1 - - - -
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Residues in contact with ASP 355 (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* 3.6 3.6 - - - -
338C GLN* 4.0 15.4 + - - +
354C LYS* 1.3 89.1 - - + +
356C GLY* 1.3 59.2 + - - +
367C PHE 3.3 7.5 + - - -
368C SER* 3.1 17.7 + - - +
6D TYR* 2.8 33.8 + - - +
45D ASN 5.4 0.9 - - - +
48D LEU* 4.1 21.4 - - + +
49D ALA* 4.0 32.9 - - - +
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Residues in contact with GLY 356 (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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336C VAL 3.3 10.1 - - - -
337C CYS* 3.6 0.9 - - - -
354C LYS 3.3 1.0 + - - -
355C ASP* 1.3 75.9 - - - +
357C ILE* 1.3 63.9 + - - -
358C MET 4.0 0.2 - - - -
366C ILE* 3.2 9.9 - - - +
367C PHE* 2.9 61.2 + - - -
48D LEU* 5.1 0.2 - - - +
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Residues in contact with ILE 357 (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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14B TYR* 4.3 20.9 - - + +
334C VAL 3.9 1.6 - - - +
335C VAL* 3.7 1.0 - - - -
336C VAL* 3.1 30.8 + - - +
356C GLY* 1.3 75.4 - - - +
358C MET* 1.3 65.8 + - - +
359C ASN* 6.3 0.2 - - + -
364C ASP* 4.4 6.7 - - - +
365C TYR 3.4 7.9 - - - +
366C ILE* 4.3 9.9 - - + -
6D TYR* 3.8 22.9 - - + -
9D THR* 4.0 34.0 - - + +
10D THR 5.5 0.2 - - - +
11D LEU* 5.6 2.5 - - + -
44D ILE* 3.8 28.0 - - + -
48D LEU* 4.1 14.8 - - + -
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Residues in contact with MET 358 (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 3.4 7.9 - - - +
335C VAL* 3.6 25.6 - - + -
357C ILE* 1.3 79.5 - - - +
359C ASN* 1.3 59.6 + - - +
360C LEU* 3.9 17.3 - - + -
364C ASP* 3.2 6.2 - - - +
365C TYR* 2.5 60.9 + - + +
366C ILE 5.0 1.8 - - - -
367C PHE* 3.3 39.5 - - + -
56D VAL* 4.0 26.7 - - + -
81D PHE* 3.9 22.9 - - + -
83D GLU* 6.0 0.4 - - - +
88D ILE* 6.0 1.6 - - + -
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Residues in contact with ASN 359 (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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331C THR* 2.6 35.7 + - - +
332C GLU 3.9 4.8 - - - +
333C ASN* 3.1 25.8 - - - -
334C VAL* 3.1 14.5 + - + +
357C ILE* 6.3 0.4 - - + -
358C MET* 1.3 72.5 - - - +
360C LEU* 1.3 58.4 + - - +
362C GLY* 3.4 15.0 + - - -
363C ARG 3.0 11.0 + - - -
364C ASP* 2.5 27.1 + - - +
9D THR* 6.6 0.2 - - - -
10D THR* 3.6 11.2 + - - +
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Residues in contact with LEU 360 (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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333C ASN* 3.6 16.8 - - + +
334C VAL 4.7 0.7 - - - +
335C VAL* 4.7 2.0 - - + -
358C MET* 3.9 25.7 - - + -
359C ASN* 1.3 78.5 - - - +
361C ASN* 1.3 68.9 + - - +
362C GLY 2.9 9.4 + - - -
363C ARG* 2.9 23.6 + - - +
365C TYR* 3.8 22.7 + - + -
81D PHE* 3.9 41.5 - - + -
88D ILE* 3.7 33.9 - - + -
90D VAL* 5.0 3.8 - - + -
93D VAL* 4.3 6.5 - - + -
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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