Contacts of the strand formed by residues 451 - 456 (chain A) in PDB entry 3GEF
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 PHE 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A GLU* 3.7 44.9 - - + -
445A VAL* 4.7 0.5 - - - +
446A ASP* 3.1 56.7 + - + +
449A GLY 3.5 1.7 - - - -
450A LYS* 1.4 83.2 + - + +
452A VAL* 1.3 79.8 - - - +
453A ARG* 4.1 4.7 - - + -
471A ARG* 5.2 0.2 + - - -
496A THR* 3.6 23.6 - - + -
497A ILE 3.2 13.0 - - - +
498A TRP* 3.8 28.3 - + + -
520A TRP* 3.7 6.0 - - - +
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Residues in contact with VAL 452 (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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442A VAL* 4.0 16.8 - - + -
444A GLU 3.5 6.1 - - - +
445A VAL* 4.6 4.5 - - + -
451A PHE* 1.3 83.3 - - - +
453A ARG* 1.3 64.4 + - - +
454A LEU* 4.2 14.1 - - + -
469A ILE* 4.4 8.7 - - + -
471A ARG* 3.8 14.4 - - - +
496A THR* 3.5 1.4 - - - -
497A ILE* 2.9 32.0 + - - +
520A TRP* 3.6 41.7 - - + -
528A THR* 3.9 22.0 - - + -
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Residues in contact with ARG 453 (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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442A VAL* 3.7 2.4 - - - +
443A GLU* 2.9 53.1 + - + +
444A GLU* 2.8 55.7 + - + +
451A PHE* 4.1 7.3 - - + -
452A VAL* 1.3 75.1 - - - +
454A LEU* 1.4 66.2 + - - +
455A ARG* 3.9 5.9 - - - +
494A VAL* 2.9 38.9 - - + +
495A VAL 3.4 4.3 - - - +
496A THR* 3.9 14.6 - - - +
457C LYS* 3.1 34.2 + - - +
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Residues in contact with LEU 454 (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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440A VAL* 3.9 9.4 - - + -
441A ALA 3.3 14.1 - - - +
442A VAL* 3.8 25.1 - - + -
443A GLU* 4.6 0.7 - - - -
452A VAL* 4.2 11.9 - - + -
453A ARG* 1.4 77.6 - - - +
455A ARG* 1.3 61.6 + - - +
464A MET* 3.9 16.6 - - + -
469A ILE* 4.2 6.1 - - + -
483A PHE* 3.5 32.1 - - + -
489A LEU* 4.4 1.5 - - + +
493A GLN 4.0 0.2 - - - +
494A VAL* 3.1 8.5 - - - +
495A VAL* 2.9 39.0 + - + -
497A ILE* 4.0 13.7 - - + -
530A LEU* 3.9 15.9 - - + -
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Residues in contact with ARG 455 (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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440A VAL* 3.3 2.1 - - - -
441A ALA* 2.9 37.0 + - + +
443A GLU* 2.8 50.3 + - + +
453A ARG* 3.9 1.2 - - - +
454A LEU* 1.3 75.2 - - - +
456A ASN* 1.3 70.8 + - - +
457A LYS* 3.4 12.4 + - + +
489A LEU* 4.1 3.8 - - - -
492A GLY 3.0 29.7 + - - -
493A GLN* 3.5 5.5 - - - +
494A VAL* 3.2 20.0 - - + +
443C GLU* 4.3 3.6 - - - +
455C ARG* 3.7 22.8 - - - +
456C ASN 4.2 1.2 + - - -
457C LYS* 3.4 29.7 + - - +
458C SER 5.4 0.4 + - - -
492C GLY* 3.9 19.8 + - - -
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Residues in contact with ASN 456 (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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439A ARG* 3.5 12.5 - - - +
440A VAL* 4.3 3.6 - - + +
455A ARG* 1.3 71.0 - - - +
457A LYS* 1.3 56.5 + - - +
458A SER* 2.8 25.6 + - - +
460A GLU 2.9 21.9 + - - -
462A GLN* 3.5 10.7 - - - +
489A LEU* 2.9 39.3 + - + +
490A LYS 3.3 21.6 + - - +
491A ALA* 3.9 3.1 - - - -
492A GLY* 2.9 32.4 + - - -
493A GLN 2.9 9.7 + - - -
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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