Contacts of the strand formed by residues 464 - 469 (chain B) in PDB entry 4G3D
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 TRP 464 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A ASP* 4.4 17.9 - - + -
391A TYR* 3.7 25.6 - + - -
430B LYS* 3.8 36.1 - - + +
431B VAL 3.5 24.2 - - - -
432B ARG* 3.5 40.4 - - + -
459B VAL 4.0 0.5 - - - +
460B ARG* 3.2 6.4 - - - +
461B GLU* 2.8 38.1 + - + +
462B GLY 3.1 2.2 - - - -
463B PRO* 1.3 100.8 - - + +
465B VAL* 1.3 62.1 + - - +
466B ASN* 4.5 14.6 - - - +
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Residues in contact with VAL 465 (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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360B TRP* 3.8 34.5 - - + -
429B LYS 3.5 3.6 - - - +
430B LYS* 3.6 2.1 - - - -
431B VAL* 2.8 45.0 + - + +
433B LEU* 3.9 27.8 - - + -
436B PHE* 3.8 36.1 - - + -
458B ALA* 4.7 0.7 - - + -
459B VAL 4.0 1.8 - - - -
460B ARG* 4.3 3.6 - - + +
464B TRP* 1.3 76.5 - - - +
466B ASN* 1.3 63.6 + - - +
467B ILE* 3.8 13.9 + - + -
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Residues in contact with ASN 466 (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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393B TYR 5.8 0.2 + - - -
395B GLU* 5.1 1.0 + - - -
399B TRP* 3.7 20.5 - - - +
428B VAL* 3.8 7.8 - - + +
429B LYS 3.8 2.2 - - - -
430B LYS* 3.4 35.7 + - - +
458B ALA* 3.1 5.2 - - - -
459B VAL* 2.8 52.1 + - - +
461B GLU* 4.2 23.8 + - - +
464B TRP* 4.5 7.3 + - - +
465B VAL* 1.3 72.5 - - - +
467B ILE* 1.3 63.5 + - - +
468B PHE* 3.7 22.0 - - + -
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Residues in contact with ILE 467 (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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427B ALA 3.5 0.7 - - - +
428B VAL* 3.2 4.5 - - - -
429B LYS* 2.6 54.4 + - + +
431B VAL* 4.0 14.4 - - + -
436B PHE* 4.4 8.7 - - + -
440B GLU* 3.4 35.4 - - - +
441B LEU* 3.8 21.3 - - + -
455B LEU* 3.7 24.9 - - + -
457B GLY 3.7 2.7 - - - -
458B ALA* 4.2 1.3 - - + -
465B VAL* 4.1 13.0 - - + +
466B ASN* 1.3 75.4 - - - +
468B PHE* 1.3 61.9 + - - +
469B MET* 4.6 10.7 - - - +
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Residues in contact with PHE 468 (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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381B LEU* 3.6 21.3 - - + -
386B LEU* 3.8 21.3 - - + -
393B TYR* 3.8 17.0 - + - -
399B TRP* 3.9 15.9 - + - -
417B MET* 3.6 30.7 - - - -
426B CYS* 4.2 2.5 - - - -
427B ALA 3.3 2.5 - - - -
428B VAL* 3.4 29.8 - - + -
455B LEU* 3.7 4.5 - - - +
456B TYR* 2.7 29.8 + - + -
457B GLY 2.7 22.9 + - - +
459B VAL* 3.7 24.9 - - + -
466B ASN* 3.7 24.0 - - + -
467B ILE* 1.3 72.7 - - - +
469B MET* 1.3 56.9 + - - +
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Residues in contact with MET 469 (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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414B VAL* 5.4 13.5 - - + -
426B CYS* 3.2 3.4 - - - +
427B ALA* 2.8 48.5 + - + +
428B VAL 5.9 0.2 - - - -
429B LYS* 4.8 19.1 - - + +
453B VAL* 4.1 19.7 - - + -
454B PRO 3.4 16.4 - - - +
455B LEU* 4.5 2.9 - - + -
456B TYR* 3.5 10.0 - - - +
467B ILE* 4.6 11.7 - - + +
468B PHE* 1.3 76.5 - - - +
470B GLU* 1.3 66.0 + - - +
522B LEU* 4.4 12.3 - - + -
533B CYS* 4.3 20.4 - - + -
534B ASP 5.5 2.2 - - - +
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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