Contacts of the strand formed by residues 497 - 502 (chain D) in PDB entry 2FGJ
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 VAL 497 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495D GLY 4.8 0.2 - - - +
496D GLU* 1.3 73.7 - - - +
498D ILE* 1.3 63.6 + - - +
645D MET* 5.6 1.8 - - + -
648D MET* 4.7 15.0 - - + -
649D HIS* 6.3 2.2 - - + -
652D CYS* 3.6 32.3 - - + -
657D VAL* 3.4 11.7 - - + +
659D ILE* 4.3 22.4 - - + -
669D ASN 5.4 2.5 - - - +
670D ALA* 3.5 17.7 - - + +
671D ASP* 2.9 45.8 + - - +
672D ARG 3.3 9.7 + - - +
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Residues in contact with ILE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D LEU* 5.7 0.2 - - + -
492D ILE* 3.4 35.4 - - + -
496D GLU* 3.5 33.0 - - + +
497D VAL* 1.3 74.5 - - - +
499D GLY* 1.3 67.2 + - - +
500D ILE* 4.7 7.0 - - + -
657D VAL 3.0 9.6 + - - +
658D ILE* 3.2 14.8 - - + +
659D ILE* 2.8 26.4 + - - +
670D ALA* 4.6 1.6 - - - -
672D ARG* 3.4 37.5 - - + +
674D ILE* 3.6 28.9 - - + -
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Residues in contact with GLY 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498D ILE* 1.3 73.5 - - - +
500D ILE* 1.3 60.4 + - - +
501D VAL 4.0 0.7 - - - -
659D ILE 3.2 8.3 - - - -
667D VAL* 3.8 22.9 - - - -
670D ALA* 4.1 3.1 - - - +
672D ARG 3.0 11.8 + - - -
673D ILE* 3.4 6.0 - - - -
674D ILE* 2.7 34.8 + - - +
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Residues in contact with ILE 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D LEU* 6.2 1.6 - - + -
498D ILE* 4.7 7.9 - - + -
499D GLY* 1.3 76.0 - - - +
501D VAL* 1.3 63.6 + - - +
508D LYS* 3.4 32.7 - - + +
511D LEU* 4.3 17.5 - - + -
512D THR* 4.3 10.1 - - + -
515D ILE* 6.4 0.4 - - + -
658D ILE* 3.6 30.1 - - + -
659D ILE 2.8 9.9 + - - +
660D ILE* 3.4 20.5 - - + -
661D ALA 3.2 23.0 + - - -
667D VAL* 4.8 0.4 - - - +
674D ILE* 3.4 13.0 - - + +
676D MET* 3.8 24.5 - - + -
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Residues in contact with VAL 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D ILE* 1.3 75.9 - - - +
502D GLY* 1.3 58.7 + - - +
508D LYS* 3.5 7.7 - - - +
661D ALA* 3.4 22.0 - - + +
664D LEU* 3.9 21.8 - - + -
667D VAL* 3.6 30.7 - - + -
673D ILE* 3.9 15.0 - - + -
674D ILE 3.0 15.9 + - - +
675D VAL* 3.3 20.0 - - + -
676D MET* 3.0 24.3 + - - +
698D TYR* 4.0 12.8 - - + -
701D LEU* 5.3 2.7 - - + -
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Residues in contact with GLY 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637C ASP* 4.1 11.2 - - - +
501D VAL* 1.3 78.3 - - - +
503D ARG* 1.3 63.6 + - - -
506D SER* 3.5 6.3 - - - -
508D LYS* 2.8 18.9 + - - +
661D ALA 4.8 2.4 + - - +
662D ALA* 5.7 1.7 - - - -
664D LEU* 5.7 0.2 - - - +
675D VAL* 4.9 0.9 - - - -
676D MET 3.5 15.5 - - - -
701D LEU* 4.5 16.3 - - - +
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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