Contacts of the strand formed by residues 398 - 404 (chain A) in PDB entry 2WIN
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 LEU 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A PHE* 3.5 28.7 - - + -
348A PHE* 5.2 2.5 - - + -
389A ILE* 4.1 19.1 - - + -
391A THR* 3.3 40.8 - - + +
396A LYS 3.5 0.6 + - - +
397A PRO* 1.3 72.0 - - - +
399A SER* 1.3 67.8 + - - +
400A ILE* 3.2 28.6 - - + +
420A GLN* 3.6 3.2 - - - -
421A ALA* 2.9 37.0 + - + -
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Residues in contact with SER 399 (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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397A PRO 3.9 3.4 + - - -
398A LEU* 1.3 81.8 - - - +
400A ILE* 1.3 62.1 + - - +
401A THR* 4.4 1.7 + - - -
418A THR* 3.8 18.2 - - - +
419A MET 3.7 5.4 + - - -
420A GLN* 4.7 6.7 - - - +
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Residues in contact with ILE 400 (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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335A PHE* 4.6 1.4 - - - -
348A PHE* 5.1 2.7 - - + -
350A LEU* 3.5 28.5 - - + -
369A VAL* 3.7 23.8 - - + -
389A ILE* 4.0 15.3 - - + -
398A LEU* 3.2 45.5 - - + +
399A SER* 1.3 74.4 + - - +
401A THR* 1.3 65.4 + - - +
402A VAL* 4.1 8.7 + - + -
417A ARG 4.1 1.0 - - - +
418A THR* 3.4 3.3 - - - +
419A MET* 3.1 54.4 + - + +
421A ALA* 4.6 7.4 - - + -
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Residues in contact with THR 401 (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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369A VAL* 3.4 3.7 - - - +
370A GLN* 2.8 61.1 + - - +
399A SER* 4.4 2.1 + - - -
400A ILE* 1.3 73.9 - - - +
402A VAL* 1.3 62.7 + - - +
403A ARG* 3.9 3.0 + - + +
416A THR* 3.3 25.8 - - - +
417A ARG 3.6 3.1 - - - +
418A THR* 2.9 29.4 + - - +
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Residues in contact with VAL 402 (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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333A ILE* 3.6 21.7 - - + +
335A PHE* 3.4 33.7 - - + -
350A LEU* 4.3 16.8 - - + -
352A VAL* 3.8 26.7 - - + -
367A VAL* 4.1 13.9 - - + -
368A ALA 3.2 15.3 - - - +
369A VAL* 5.1 1.1 - - - -
387A LEU* 4.3 3.6 - - + -
400A ILE* 4.1 4.2 - - + -
401A THR* 1.3 75.0 - - - +
403A ARG* 1.3 62.3 + - - +
416A THR* 3.4 15.7 + - - -
417A ARG 3.2 16.5 + - - -
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Residues in contact with ARG 403 (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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367A VAL* 4.6 0.2 - - - -
368A ALA* 3.0 31.4 + - - +
369A VAL 5.3 4.0 - - - +
370A GLN* 5.7 10.0 - - - +
401A THR* 3.9 5.2 + - + +
402A VAL* 1.3 76.4 - - - +
404A THR* 1.3 75.7 + - + +
405A LYS* 3.5 29.0 + - - +
411A GLU* 2.7 53.5 + - - +
414A GLN* 4.3 15.0 + - + +
415A ALA 4.5 2.7 - - - -
416A THR* 4.0 28.7 + - - +
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Residues in contact with THR 404 (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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331A TYR* 4.6 12.1 - - + -
333A ILE* 4.1 10.5 - - + +
354A VAL* 5.9 1.3 - - - -
365A VAL* 3.6 20.4 - - - +
366A PRO 3.6 7.2 - - - -
367A VAL* 4.3 6.1 - - - -
403A ARG* 1.3 83.2 - - - +
405A LYS* 1.3 62.8 + - - +
406A LYS* 3.6 7.3 + - - +
414A GLN* 3.1 44.7 + - + +
415A ALA* 3.1 40.3 + - + +
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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