Contacts of the helix formed by residues 595 - 602 (chain D) in PDB entry 2GL7
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 THR 595 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537D VAL* 4.7 16.5 - - - +
540D LEU* 5.2 2.3 - - - +
590D ILE* 3.0 37.5 - - + +
591D ARG* 4.1 2.4 + - - -
593D LEU* 4.0 7.2 - - - -
594D ASN* 1.3 75.5 - - - +
596D ILE* 1.3 75.9 + - + +
597D PRO* 3.4 2.0 - - - -
598D LEU* 3.0 25.2 + - - +
599D PHE* 3.1 44.8 + - + -
621D LEU* 4.5 0.9 - - + -
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Residues in contact with ILE 596 (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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591D ARG* 4.7 17.9 - - + +
595D THR* 1.3 90.8 - - + +
597D PRO* 1.3 69.2 - - + +
599D PHE* 3.4 6.8 + - - +
600D VAL* 3.3 25.7 + - + +
618D LEU* 4.4 3.8 - - + -
621D LEU* 4.3 14.6 - - + -
627D ALA* 4.3 21.3 - - + +
630D ALA* 4.1 36.3 - - + +
631D ILE* 3.9 27.6 - - + -
634D GLU* 4.8 2.7 - - - +
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Residues in contact with PRO 597 (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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594D ASN* 3.5 32.3 - - - +
595D THR 3.4 4.0 - - - -
596D ILE* 1.3 95.5 - - + +
598D LEU* 1.3 59.7 + - - +
600D VAL* 3.8 1.4 + - - +
601D GLN* 3.3 31.4 + - - +
634D GLU* 3.6 36.6 - - + +
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Residues in contact with LEU 598 (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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540D LEU* 3.9 30.5 - - + -
541D VAL* 4.3 28.7 - - + +
544D HIS* 3.5 33.4 - - + -
594D ASN 4.9 2.0 + - - +
595D THR* 3.0 18.9 + - - +
597D PRO* 1.3 78.1 - - - +
599D PHE* 1.3 66.4 + - + +
601D GLN* 3.2 15.4 + - + +
602D LEU* 3.2 20.6 + - + +
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Residues in contact with PHE 599 (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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540D LEU* 3.6 27.8 - - + -
574D THR* 3.9 19.7 - - + -
577D LEU* 4.1 19.3 - - + -
590D ILE* 4.3 3.4 - - + -
595D THR* 3.1 48.0 + - + -
596D ILE* 3.4 2.0 + - - +
598D LEU* 1.3 76.9 - - + +
600D VAL* 1.3 61.6 + - - +
602D LEU* 3.3 19.3 + - + +
603D LEU* 3.5 18.0 + - - +
614D ALA* 3.9 5.5 - - + +
617D VAL* 3.8 31.4 - - + -
618D LEU* 3.5 35.0 - - + -
621D LEU* 4.2 8.3 - - + -
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Residues in contact with VAL 600 (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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596D ILE* 3.3 23.2 + - + +
597D PRO 3.9 4.5 - - - +
598D LEU 3.2 0.4 - - - -
599D PHE* 1.3 75.9 - - - +
601D GLN* 1.3 72.0 + - - +
603D LEU* 3.2 25.4 + - + +
604D TYR* 4.1 2.4 + - - +
618D LEU* 4.2 12.1 - - + -
631D ILE* 4.7 2.0 - - + +
634D GLU* 4.1 34.3 - - + +
635D GLY 4.7 2.2 - - - +
636D ALA* 3.9 33.0 - - + -
639D PRO* 4.8 9.3 - - + +
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Residues in contact with GLN 601 (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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544D HIS* 4.3 18.9 + - + +
597D PRO* 3.3 20.9 + - - +
598D LEU* 3.2 13.1 + - + +
600D VAL* 1.3 86.2 - - - +
602D LEU* 1.3 62.0 + - - +
604D TYR* 3.4 19.1 + - - +
605D SER* 4.2 2.4 + - - -
634D GLU* 5.7 2.8 - - - +
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Residues in contact with LEU 602 (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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540D LEU* 4.2 0.7 - - + -
544D HIS* 3.4 43.1 - - + +
570D VAL* 3.8 24.7 - - + -
574D THR* 3.9 24.0 - - + +
598D LEU* 3.2 24.9 + - + +
599D PHE* 3.5 13.9 - - + +
600D VAL 3.1 1.0 - - - -
601D GLN* 1.3 74.7 - - - +
603D LEU* 1.3 63.3 + - - +
604D TYR 3.2 2.7 - - - -
605D SER* 3.2 23.0 + - - -
610D ILE* 3.7 22.5 - - + +
611D GLN* 4.2 7.4 - - - +
614D ALA* 3.9 9.9 - - + -
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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