Contacts of the strand formed by residues 491 - 494 (chain B) in PDB entry 5N4D
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 ALA 491 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B ALA 4.0 0.2 + - - -
490B ALA* 1.3 73.5 - - - +
492B ILE* 1.3 71.0 + - - +
493B GLN 3.9 0.2 - - - -
521B ILE* 3.2 31.0 - - + +
523B ALA* 5.2 1.3 - - + -
560B LEU* 4.0 18.2 - - + -
566B ALA* 3.9 13.2 - - + +
570B LYS 2.9 9.7 + - - +
571B VAL* 4.4 4.7 - - + -
572B ALA* 2.8 27.3 + - - +
722B LEU* 4.4 0.5 - - - +
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ALA* 5.2 0.4 - - + -
491B ALA* 1.3 81.9 - - - +
493B GLN* 1.3 65.5 + - - +
494B TYR* 5.3 0.9 - - + -
514B PHE* 3.4 36.6 - - + -
515B LEU* 5.6 1.8 - - + -
520B ALA* 4.6 2.9 - - + -
521B ILE 2.9 12.3 + - - +
522B PHE* 3.4 25.5 - - + -
523B ALA 2.9 23.1 + - - -
572B ALA* 3.5 6.7 - - + +
574B ASN* 4.9 6.3 - - + -
715B TRP* 3.6 42.2 - - + -
718B ILE* 4.2 16.8 - - + -
722B LEU* 5.1 3.4 - - + -
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Residues in contact with GLN 493 (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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491B ALA 3.9 0.4 - - - -
492B ILE* 1.3 73.0 - - - +
494B TYR* 1.3 60.8 + - - +
523B ALA* 3.3 12.3 - - + +
525B PRO* 4.0 10.8 - - + -
553B PHE* 2.9 61.3 + - + -
556B ALA* 3.7 12.0 - - - +
557B ALA* 3.3 29.6 + - - +
560B LEU* 3.5 12.0 - - + +
571B VAL* 3.9 7.7 - - + +
572B ALA 2.7 15.7 + - - +
573B ILE* 3.2 14.6 - - + +
574B ASN 3.0 23.7 + - - +
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Residues in contact with TYR 494 (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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492B ILE* 4.0 1.1 + - + -
493B GLN* 1.3 74.6 - - - +
495B GLY* 1.3 66.8 + - - +
496B TYR* 5.9 2.3 - - + -
506B PHE* 4.9 6.5 - + - -
511B ILE* 6.2 0.9 - - + -
522B PHE* 3.7 34.1 - + + -
523B ALA 2.9 8.9 + - - +
524B VAL* 3.9 8.7 - - + +
525B PRO* 3.4 22.2 - - - +
553B PHE* 3.8 2.9 - - - -
574B ASN* 3.3 25.6 - - + +
575B GLY* 4.0 8.5 - - - -
576B ALA* 4.6 7.6 + - - +
715B TRP* 5.8 1.6 - + - -
9D TRP* 3.1 64.3 + + - -
10D THR* 5.0 2.4 - - + -
13D HIS* 3.1 42.2 + + - -
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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