Contacts of the strand formed by residues 438 - 443 (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 TYR 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B GLU* 6.1 0.4 - - + -
38B PRO* 5.3 6.1 - - + +
431B PRO* 4.1 3.5 - - - +
432B ASP* 3.2 39.0 + - + +
435B LYS* 3.5 28.0 + - + +
436B ASN 3.3 3.0 - - - +
437B ILE* 1.3 95.4 - - + +
439B ILE* 1.3 61.3 + - - +
440B TYR* 5.8 0.2 - - + -
449B ARG* 3.5 54.0 + - + +
450B ILE 3.4 15.7 - - - -
451B ARG* 3.4 47.2 + - + -
452B VAL* 3.9 5.7 - - - +
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Residues in contact with ILE 439 (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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380B TYR* 4.2 13.9 - - + -
391B PHE* 3.8 41.1 - - + -
399B LEU* 4.0 23.3 - - + -
429B LEU* 4.3 18.2 - - + -
430B VAL 3.7 15.3 - - - +
431B PRO* 4.2 3.4 - - + -
432B ASP 4.4 0.7 - - - +
438B TYR* 1.3 76.0 - - - +
440B TYR* 1.3 74.4 + - - +
441B LEU 3.6 1.0 + - - -
449B ARG* 4.9 0.2 - - - -
450B ILE* 2.8 40.4 + - + +
452B VAL* 4.3 17.0 - - + -
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Residues in contact with TYR 440 (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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49B ILE* 5.4 4.0 - - + -
51B ALA* 4.6 3.8 - - + -
57B VAL* 3.8 26.0 - - + -
70B TYR* 2.8 33.7 + - - +
72B LEU* 3.6 29.6 - - + -
428B LYS 4.7 0.7 - - - +
429B LEU* 4.1 9.9 - - - +
430B VAL* 2.7 51.3 + - + +
431B PRO 4.1 7.6 - - - -
432B ASP* 3.4 35.6 + - + -
433B PRO* 4.8 0.7 - - + -
439B ILE* 1.3 72.0 - - - +
441B LEU* 1.3 61.1 + - - +
442B THR* 3.9 5.0 + - - +
447B VAL* 4.4 10.5 - - + -
448B ARG 3.4 12.1 - - - +
449B ARG* 3.6 21.3 + - + -
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Residues in contact with LEU 441 (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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397B GLY 5.0 1.8 - - - +
399B LEU* 4.4 25.8 - - + -
417B TYR* 3.8 31.4 - - + -
419B ILE* 4.2 18.6 - - + -
425B VAL* 3.4 37.0 - - + -
429B LEU* 3.9 13.5 - - + -
439B ILE 3.6 1.6 + - - -
440B TYR* 1.3 71.9 - - - +
442B THR* 1.3 63.5 + - - +
446B GLU 3.8 0.9 - - - +
447B VAL* 3.4 2.0 - - - -
448B ARG* 2.7 43.2 + - + +
450B ILE* 3.3 22.4 - - + -
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Residues in contact with THR 442 (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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46B ILE* 3.8 38.4 - - + -
49B ILE* 4.0 16.7 - - + +
425B VAL* 3.4 9.0 - - - +
426B PHE* 2.8 52.9 + - + +
428B LYS 4.6 6.7 + - - -
429B LEU* 5.2 0.4 - - - +
440B TYR* 3.9 4.9 + - - +
441B LEU* 1.3 78.2 + - - +
443B ALA* 1.3 69.3 + - - +
444B GLY 5.1 0.4 - - - +
446B GLU 3.4 3.1 - - - -
447B VAL* 3.9 15.6 - - - +
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Residues in contact with ALA 443 (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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419B ILE* 3.7 30.5 - - + -
423B THR* 3.7 13.5 - - - +
424B PRO 3.4 20.6 - - - +
425B VAL* 4.1 0.9 - - - -
426B PHE* 4.2 2.5 - - - +
441B LEU* 5.5 0.4 - - + -
442B THR* 1.3 79.8 - - - +
444B GLY* 1.3 66.9 + - - +
445B LYS 3.0 0.3 + - - -
446B GLU* 2.9 31.2 + - + +
448B ARG* 6.3 0.4 - - - +
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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