Contacts of the strand formed by residues 508 - 513 (chain D) in PDB entry 4JF7
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 ILE 508 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439D GLN* 3.9 26.1 - - + +
440D VAL* 4.1 18.2 - - + -
441D PRO* 5.2 1.3 - - + -
488D TYR* 3.7 33.9 - - + +
501D TYR* 4.0 5.2 - - + -
502D ILE 3.5 13.0 - - - +
503D ALA* 4.1 2.2 - - + +
507D GLN* 1.3 75.9 - - - +
509D ILE* 1.3 63.2 + - - +
510D SER 3.6 15.9 - - - +
511D SER* 4.0 17.3 - - - +
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Residues in contact with ILE 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLY 3.8 22.7 - - - +
138D ARG* 4.2 14.4 - - - +
140D LEU 4.0 18.9 - - - +
141D THR* 5.0 1.7 + - - -
483D THR* 4.8 4.7 - - + -
502D ILE* 2.8 30.1 + - + +
503D ALA 4.5 2.9 - - - +
504D ASN* 4.3 20.2 - - + +
507D GLN* 3.8 17.7 + - + +
508D ILE* 1.3 76.8 - - - +
510D SER* 1.3 63.0 + - - +
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Residues in contact with SER 510 (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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140D LEU 4.2 2.0 - - - -
141D THR* 3.3 18.7 + - - -
142D LEU* 2.8 37.7 + - - +
501D TYR* 3.1 4.4 - - - +
502D ILE* 2.6 45.0 + - - +
508D ILE* 3.6 1.9 - - - +
509D ILE* 1.3 79.6 - - - +
511D SER* 1.3 63.8 + - - +
512D GLN* 5.4 2.8 + - - -
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Residues in contact with SER 511 (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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142D LEU* 4.3 0.7 - - - -
488D TYR* 5.8 0.7 - - - -
499D THR* 4.1 13.2 - - - -
500D MET 3.2 9.6 - - - -
501D TYR* 4.4 1.6 - - - -
508D ILE* 4.0 17.3 - - - +
510D SER* 1.3 80.0 + - - +
512D GLN* 1.3 78.4 + - - +
513D GLN 4.3 0.4 - - - -
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Residues in contact with GLN 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 4.1 21.6 + - + +
499D THR* 3.6 3.4 - - - -
500D MET* 2.8 32.5 + - - +
510D SER* 5.4 2.2 + - - -
511D SER* 1.3 86.4 + - - +
513D GLN* 1.3 67.2 + - - +
514D PHE 3.6 0.9 + - - -
560D ARG* 3.9 33.3 + - - +
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Residues in contact with GLN 513 (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 ASN* 5.0 6.9 + - - -
497D ASN* 3.6 37.6 + - - +
498D PRO 3.5 13.5 - - - +
499D THR* 3.7 16.0 + - + +
512D GLN* 1.3 75.6 + - - +
514D PHE* 1.3 68.6 + - - +
515D GLY 4.0 8.5 + - - +
516D SER 4.0 5.5 + - - -
517D SER* 3.8 21.4 - - - +
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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