Contacts of the strand formed by residues 350 - 355 (chain A) 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 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ILE* 3.5 4.7 - - - -
347A LYS* 3.0 30.9 + - - +
348A GLU 3.7 1.2 - - - -
349A ASN* 1.3 81.4 + - - +
351A ILE* 1.3 72.3 + - - +
352A TYR* 3.6 33.5 + - + +
363A SER* 4.0 12.6 - - - +
364A ALA 3.4 14.6 - - - +
365A GLN* 3.2 25.8 + - - +
370A LEU* 3.6 4.3 - - - +
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Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 5.9 1.6 - - + -
18A TRP* 5.9 2.7 - - + -
344A TYR* 4.9 2.0 - - + -
345A PHE 5.5 0.2 - - - -
346A ILE* 4.0 5.6 - - + -
350A THR* 1.3 73.7 - - - +
352A TYR* 1.3 74.2 + - - +
363A SER* 3.2 5.0 - - - -
364A ALA* 2.8 42.0 + - + +
366A VAL* 4.1 13.9 - - + -
370A LEU* 3.7 21.1 - - + -
381A PHE* 3.3 52.9 - - + -
392A PRO* 4.0 27.4 - - + -
394A MET* 3.2 12.0 - - + +
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Residues in contact with TYR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A PRO* 3.5 29.2 - - + +
343A ILE 4.4 0.2 - - - -
344A TYR* 3.4 10.9 - - - +
345A PHE* 2.8 77.0 + + + +
346A ILE* 4.3 0.7 - - - -
347A LYS* 3.7 22.7 - - + +
350A THR* 3.6 35.8 + - + +
351A ILE* 1.3 78.6 - - - +
353A SER* 1.3 62.5 + - - +
361A THR* 4.4 9.6 - - + -
362A ARG 3.2 8.3 - - - +
363A SER* 3.9 22.2 - - - -
394A MET* 3.7 2.2 - - - -
397A ILE* 5.3 3.8 - - + -
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A ARG* 4.2 16.9 + - - -
343A ILE 3.3 6.1 - - - -
344A TYR* 3.7 26.0 - - - -
345A PHE* 4.9 0.7 - - - -
352A TYR* 1.3 75.5 - - - +
354A PHE* 1.3 59.8 + - - +
355A ASP 4.1 0.4 - - - -
360A GLN 3.6 1.4 - - - +
361A THR* 3.2 6.4 - - - -
362A ARG* 2.9 41.3 + - - +
394A MET* 3.6 18.7 - - - +
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Residues in contact with PHE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A PRO* 4.1 10.5 - - + -
319A ILE 5.6 2.0 - - - -
320A PHE* 3.6 63.5 - + + -
341A TYR 3.9 0.2 - - - +
342A ARG* 3.5 5.5 - - - -
343A ILE* 2.8 49.7 + - + +
345A PHE* 4.5 3.1 - - + -
353A SER* 1.3 73.4 - - - +
355A ASP* 1.3 74.6 + - - +
356A THR* 3.7 17.1 + - + -
359A LYS* 3.6 38.1 - - + -
360A GLN 3.4 4.9 - - - -
361A THR* 3.1 23.8 - - - +
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Residues in contact with ASP 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LYS* 2.5 39.7 + - - +
341A TYR 4.0 2.7 - - - -
342A ARG* 3.0 26.2 + - - +
353A SER 4.1 0.8 - - - -
354A PHE* 1.3 74.6 - - - +
356A THR* 1.3 56.0 + - - +
357A LYS* 3.0 33.8 + - - +
358A SER* 3.2 20.8 + - - +
359A LYS* 2.8 34.0 + - - -
360A GLN* 2.9 14.7 + - + +
362A ARG* 5.0 0.7 - - - +
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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