Contacts of the helix formed by residues 624 - 634 (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 ASP 624 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587D ARG* 5.9 7.0 - - + +
621D LEU 3.5 10.0 + - - +
622D ALA 3.1 14.2 - - - +
623D GLN* 1.3 79.4 - - - +
625D LYS* 1.3 63.2 + - - +
626D GLU* 3.5 4.9 - - + +
627D ALA* 3.7 8.3 + - + +
628D ALA* 3.6 13.3 + - - +
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Residues in contact with LYS 625 (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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622D ALA 5.3 0.2 - - - -
623D GLN 4.2 0.6 + - - -
624D ASP* 1.3 72.0 - - - +
626D GLU* 1.3 63.7 + - - +
628D ALA* 3.4 15.9 + - - +
629D GLU* 3.4 19.7 - - - +
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Residues in contact with GLU 626 (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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624D ASP* 3.5 3.2 - - + +
625D LYS* 1.3 78.1 - - - +
627D ALA* 1.3 61.0 + - - +
629D GLU* 2.7 24.3 - - - +
630D ALA* 3.4 13.3 + - - +
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Residues in contact with ALA 627 (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* 5.4 7.9 - - + -
596D ILE* 4.3 16.3 - - + +
621D LEU* 3.4 33.9 - - + +
622D ALA* 5.1 0.2 - - - -
624D ASP* 3.7 9.4 + - + +
625D LYS 3.3 0.6 - - - -
626D GLU* 1.3 77.2 - - - +
628D ALA* 1.3 61.9 + - - +
629D GLU 3.5 0.2 - - - -
630D ALA* 4.0 9.6 - - - +
631D ILE* 3.3 27.1 + - - +
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Residues in contact with ALA 628 (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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622D ALA* 4.4 13.7 - - - +
624D ASP 3.6 12.0 + - - +
625D LYS* 3.4 13.2 + - - +
626D GLU 3.2 0.8 - - - -
627D ALA* 1.3 78.5 - - - +
629D GLU* 1.3 60.0 + - + +
631D ILE* 3.2 26.9 - - - +
632D GLU* 3.2 3.1 + - - +
661D ARG 3.8 22.2 - - - +
662D MET* 3.5 18.1 - - + +
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Residues in contact with GLU 629 (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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625D LYS* 3.4 18.8 - - - +
626D GLU* 2.7 30.6 - - - +
628D ALA* 1.3 75.1 - - + +
630D ALA* 1.3 62.3 + - - +
631D ILE 3.1 0.9 - - - -
632D GLU* 3.5 12.1 - - + +
633D ALA* 2.8 29.1 + - - +
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Residues in contact with ALA 630 (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* 4.1 23.2 - - + +
626D GLU 3.4 17.8 + - - +
627D ALA* 4.0 7.2 - - - +
629D GLU* 1.3 76.3 + - - +
631D ILE* 1.3 60.5 + - - +
633D ALA* 3.8 5.7 + - - +
634D GLU* 3.2 28.4 + - - +
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Residues in contact with ILE 631 (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* 3.9 20.6 - - + +
600D VAL* 4.8 1.1 - - + -
618D LEU* 3.7 51.6 - - + +
621D LEU* 5.2 4.9 - - + -
622D ALA* 4.8 9.2 - - + -
627D ALA 3.3 14.0 + - - +
628D ALA* 3.2 15.5 - - - +
630D ALA* 1.3 77.5 - - - +
632D GLU* 1.3 67.3 + - - +
633D ALA 3.2 0.2 - - - -
634D GLU* 3.3 12.1 + - - +
636D ALA* 3.2 35.1 + - + +
640D LEU* 6.1 2.2 - - + -
658D VAL* 5.0 9.0 - - + +
662D MET* 4.1 14.1 - - + -
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Residues in contact with GLU 632 (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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628D ALA 3.2 5.0 + - - +
629D GLU* 3.3 20.1 + - + +
631D ILE* 1.3 83.4 - - + +
633D ALA* 1.3 62.8 + - - +
635D GLY* 3.1 15.2 + - - -
636D ALA 4.9 2.9 - - - +
637D THR* 5.0 11.8 + - - +
662D MET* 5.4 5.4 - - + -
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Residues in contact with ALA 633 (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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629D GLU 2.8 17.5 + - - +
630D ALA* 4.0 9.6 - - - +
631D ILE 3.2 0.6 - - - -
632D GLU* 1.3 76.4 - - - +
634D GLU* 1.3 63.4 + - - +
635D GLY 3.2 1.6 + - - -
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Residues in contact with GLU 634 (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* 4.8 2.1 - - + +
597D PRO* 3.6 48.2 - - + +
600D VAL* 4.1 26.2 - - + +
601D GLN* 5.7 3.1 - - - +
630D ALA* 3.2 20.0 + - - +
631D ILE 3.3 9.8 + - - +
632D GLU 3.2 1.2 - - - -
633D ALA* 1.3 80.3 - - - +
635D GLY* 1.3 61.7 + - - +
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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