Contacts of the strand formed by residues 388 - 394 (chain B) in PDB entry 3NVN
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 THR 388 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B VAL* 4.5 8.7 - - + -
303B LEU* 3.2 34.5 - - + +
330B LEU* 5.1 1.8 - - + -
382B THR 3.5 9.2 - - - +
383B VAL* 4.5 5.0 - - - +
386B ASN 4.2 1.4 + - - -
387B ARG* 1.3 72.3 - - - +
389B VAL* 1.3 61.8 + - - +
390B LEU* 4.3 17.0 - - + -
402B VAL 3.6 1.6 - - - +
403B ILE* 3.5 3.8 - - - +
404B LEU* 3.0 62.5 + - + +
408B LEU* 3.7 8.5 - - - +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B TYR 3.7 0.9 - - - +
381B GLY* 3.2 5.0 - - - -
382B THR* 2.7 41.0 + - - +
384B VAL* 3.3 31.9 - - + -
387B ARG 4.0 3.6 - - - +
388B THR* 1.3 77.4 - - - +
390B LEU* 1.3 64.0 + - - +
391B PHE* 3.7 22.9 - - + -
401B LYS* 3.6 32.5 - - + -
402B VAL 3.6 3.6 - - - +
403B ILE* 4.5 8.7 - - + -
470B PRO* 4.0 17.0 - - + -
471B HIS* 4.5 3.4 - - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B VAL* 4.7 3.1 - - + -
307B ALA* 4.3 19.5 - - + -
328B LEU* 3.6 24.2 - - + -
330B LEU* 4.1 23.1 - - + -
369B SER 5.6 0.7 - - - +
379B VAL* 4.6 4.7 - - + -
380B TYR 3.5 2.0 - - - +
381B GLY* 3.6 24.7 - - - +
388B THR* 4.3 13.5 - - + -
389B VAL* 1.3 77.9 - - - +
391B PHE* 1.3 64.2 + - - +
392B LEU* 3.6 14.4 - - + +
401B LYS* 3.3 4.0 - - - +
402B VAL* 2.8 46.7 + - + +
404B LEU* 4.2 18.8 - - + -
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Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B VAL* 3.2 6.6 - - - -
380B TYR* 2.8 57.5 + + + +
382B THR* 4.5 9.2 - - - -
389B VAL* 3.7 24.7 - - + -
390B LEU* 1.3 72.6 - - - +
392B LEU* 1.3 63.0 + - - +
399B LEU* 4.2 12.8 - - + -
400B LEU 3.3 10.3 - - - +
401B LYS* 3.9 18.4 - - + -
416B ILE* 5.7 2.5 - - + -
429B LEU* 3.4 9.6 - - + +
439B ILE* 3.8 25.6 - - + -
452B VAL* 3.7 49.6 - - + -
471B HIS* 4.3 4.9 - - - -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B VAL* 4.6 4.5 - - + -
328B LEU* 4.0 17.7 - - + -
371B LEU* 4.3 16.2 - - + -
376B LEU* 4.2 17.9 - - + -
378B SER 3.3 7.9 - - - +
379B VAL* 3.5 24.2 - - + -
390B LEU* 3.6 21.8 - - + +
391B PHE* 1.3 81.5 - - - +
393B GLY* 1.3 60.3 + - - +
398B GLN 3.4 0.9 - - - +
399B LEU* 3.2 10.6 - - - +
400B LEU* 2.7 52.8 + - + +
402B VAL* 3.8 24.2 - - + -
429B LEU* 4.4 0.7 - - - -
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Residues in contact with GLY 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B LEU* 3.4 7.4 - - - +
377B THR* 2.9 26.6 + - - -
378B SER* 2.9 20.3 + - - +
392B LEU* 1.3 75.0 - - - +
394B THR* 1.3 64.4 + - - +
398B GLN 3.5 5.2 - - - -
399B LEU* 4.8 2.7 - - - -
425B VAL* 3.9 19.1 - - - -
429B LEU* 4.3 1.1 - - - +
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Residues in contact with THR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B HIS* 4.1 13.7 - - + +
375B ASP* 3.1 15.3 - - - +
376B LEU* 4.2 2.5 - - + -
377B THR* 3.7 6.1 - - - -
393B GLY* 1.3 78.7 - - - +
395B GLY* 1.3 62.3 + - - +
396B ASP* 2.7 26.3 + - - +
397B GLY 3.4 1.0 + - - -
398B GLN* 2.9 32.2 + - + +
400B LEU* 3.5 31.4 - - + -
425B VAL* 3.1 28.0 + - - +
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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