Contacts of the helix formed by residues 531 - 549 (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 GLY 531 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495D VAL* 4.3 2.9 - - - +
499D HIS* 4.7 3.5 + - - -
528D ARG 3.0 12.7 + - - -
529D GLU 3.3 1.4 + - - -
530D GLN* 1.3 80.8 - - - +
532D ALA* 1.3 65.7 + - - +
533D ILE 3.4 2.6 + - - -
534D PRO* 3.7 16.2 - - - +
535D ARG* 3.6 22.0 + - - +
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Residues in contact with ALA 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D VAL* 4.1 24.0 - - + -
498D LEU* 4.5 4.3 - - - +
514D ILE* 5.0 9.0 - - + -
527D LEU* 3.2 32.6 + - + +
528D ARG* 4.3 1.0 + - - +
530D GLN 3.6 0.4 - - - -
531D GLY* 1.3 77.8 - - - +
533D ILE* 1.3 60.8 + - + +
535D ARG* 3.5 1.4 + - - +
536D LEU* 2.9 44.2 + - + +
580D LEU* 5.2 2.5 - - + -
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Residues in contact with ILE 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D LEU 6.2 0.2 - - - -
528D ARG* 5.2 10.7 - - + +
532D ALA* 1.3 75.6 - - + +
534D PRO* 1.3 73.8 - - + +
536D LEU* 3.1 8.2 + - - +
537D VAL* 3.0 24.0 + - + +
577D LEU* 4.3 7.4 - - + -
580D LEU* 4.3 19.7 - - + -
586D ASN* 4.2 22.7 - - + +
589D VAL* 3.7 25.8 - - + -
590D ILE* 3.7 27.8 - - + -
593D LEU* 3.9 9.2 - - + -
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Residues in contact with PRO 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528D ARG* 5.8 0.7 - - + +
531D GLY* 3.7 19.1 - - - +
533D ILE* 1.3 97.8 - - + +
535D ARG* 1.3 57.5 + - - +
537D VAL* 3.4 3.6 + - + +
538D GLN* 3.0 36.8 + - - +
589D VAL* 4.6 8.7 - - + -
593D LEU* 4.0 26.0 - - + -
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Residues in contact with ARG 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D LEU* 3.0 46.5 + - + -
499D HIS* 3.4 46.8 + - + +
500D PRO* 3.9 16.1 - - - +
507D ILE* 4.9 4.6 - - - +
531D GLY 3.6 16.7 + - - +
532D ALA 3.5 3.5 + - - +
533D ILE 3.2 0.4 - - - -
534D PRO* 1.3 75.0 - - - +
536D LEU* 1.3 65.3 + - - +
538D GLN* 3.3 28.5 + - - +
539D LEU* 3.1 45.2 + - - +
542D ARG* 3.3 26.3 - - - +
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Residues in contact with LEU 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D LEU* 4.2 16.4 - - + -
511D VAL* 4.1 37.7 - - + -
514D ILE* 4.3 11.7 - - + -
532D ALA* 2.9 25.9 + - + +
533D ILE 3.1 4.5 + - - +
535D ARG* 1.3 77.0 - - - +
537D VAL* 1.3 56.7 + - - +
539D LEU* 3.5 3.5 + - + -
540D LEU* 3.1 25.3 + - - +
573D CYS* 3.7 21.0 - - - +
576D ALA* 3.9 15.5 - - + -
577D LEU* 4.3 16.7 - - + +
580D LEU* 3.7 29.2 - - + -
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Residues in contact with VAL 537 (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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533D ILE* 3.0 17.4 + - + +
534D PRO* 3.6 10.1 - - + +
536D LEU* 1.3 74.5 - - - +
538D GLN* 1.3 67.8 + - + +
539D LEU 3.2 0.4 - - - -
540D LEU* 3.2 9.6 + - + +
541D VAL* 3.0 32.8 + - + +
577D LEU* 4.1 23.3 - - + -
590D ILE* 5.6 3.8 - - + +
593D LEU* 4.2 37.5 - - + +
595D THR* 4.7 17.0 - - - +
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Residues in contact with GLN 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D HIS* 5.8 0.6 - - - -
534D PRO* 3.0 22.1 + - - +
535D ARG* 3.3 41.1 - - - +
537D VAL* 1.3 80.5 - - + +
539D LEU* 1.3 59.4 + - - +
541D VAL* 3.6 5.8 + - - +
542D ARG* 3.2 48.2 + - - +
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Residues in contact with LEU 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D LEU* 3.9 28.0 - - + +
504D TRP* 4.2 23.5 - - + -
507D ILE* 3.8 26.5 - - + -
511D VAL* 4.5 2.7 - - + -
535D ARG* 3.1 50.0 + - - +
536D LEU* 3.8 2.9 - - - +
537D VAL 3.2 0.2 - - - -
538D GLN* 1.3 74.4 - - - +
540D LEU* 1.3 66.5 + - - +
542D ARG* 3.5 9.6 + - - +
543D ALA* 3.2 25.8 + - - +
569D ILE* 3.9 5.3 - - + +
573D CYS* 3.6 22.2 - - - -
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Residues in contact with LEU 540 (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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536D LEU 3.1 15.4 + - - +
537D VAL* 3.4 12.1 - - + +
539D LEU* 1.3 77.1 - - - +
541D VAL* 1.3 62.2 + - + +
543D ALA* 4.1 1.3 - - - +
544D HIS* 3.1 20.2 + - + +
569D ILE* 5.1 2.0 - - - -
570D VAL* 4.1 24.2 - - + -
573D CYS* 4.0 14.3 - - + -
574D THR* 3.4 26.9 - - - +
577D LEU* 4.3 10.8 - - + -
595D THR* 5.2 2.2 - - - +
598D LEU* 3.9 26.9 - - + -
599D PHE* 3.6 26.9 - - + -
602D LEU* 4.2 0.7 - - + -
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Residues in contact with VAL 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D VAL* 3.0 28.1 + - + +
538D GLN* 4.0 6.1 - - - +
539D LEU 3.3 0.2 - - - -
540D LEU* 1.3 77.4 - - + +
542D ARG* 1.3 65.0 + - + +
544D HIS* 3.5 6.1 + - - +
545D GLN* 3.3 43.4 + - - +
598D LEU* 4.3 25.7 - - + +
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Residues in contact with ARG 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D PRO* 5.8 2.4 - - - +
504D TRP* 5.0 12.8 - - + -
535D ARG* 3.3 35.5 - - - +
538D GLN* 3.2 35.7 + - - +
539D LEU* 3.8 12.5 - - - +
540D LEU 3.2 0.4 - - - -
541D VAL* 1.3 79.0 - - + +
543D ALA* 1.3 66.0 + - - +
545D GLN* 3.4 12.9 + - - +
546D ASP* 3.1 31.7 + - - +
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Residues in contact with ALA 543 (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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504D TRP* 4.8 2.2 - - + -
539D LEU 3.2 5.9 + - - +
540D LEU 4.2 0.4 - - - +
542D ARG* 1.3 79.9 - - - +
544D HIS* 1.3 61.9 + - - +
546D ASP* 3.3 6.5 + - - -
547D THR* 3.0 17.7 + - - -
566D MET* 3.5 43.2 - - - +
569D ILE* 3.5 32.3 - - + -
570D VAL* 3.9 7.2 - - + -
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Residues in contact with HIS 544 (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* 3.1 21.4 + - + +
541D VAL* 3.6 6.7 - - - +
543D ALA* 1.3 77.0 - - - +
545D GLN* 1.3 59.4 + - + +
546D ASP 3.1 0.2 - - - -
547D THR* 3.1 18.1 + - - -
548D GLN* 3.1 37.1 + - - -
570D VAL* 3.7 14.2 - - + +
598D LEU* 3.5 25.4 - - + -
601D GLN* 4.3 19.5 - - + +
602D LEU* 3.4 33.0 - - + +
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Residues in contact with GLN 545 (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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541D VAL* 3.4 33.6 + - - +
542D ARG* 3.5 15.1 - - - +
544D HIS* 1.3 79.9 - - + +
546D ASP* 1.3 62.4 + - - +
547D THR 3.2 2.5 + - - -
548D GLN* 4.5 12.8 - - - +
549D ARG* 4.1 21.5 + - - +
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Residues in contact with ASP 546 (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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504D TRP* 5.4 4.9 + - - -
542D ARG* 3.1 21.7 + - - +
543D ALA* 3.7 8.5 - - - +
544D HIS 3.1 1.0 - - - -
545D GLN* 1.3 81.2 - - - +
547D THR* 1.3 59.4 - - - +
549D ARG 4.8 9.5 - - - -
566D MET* 4.1 25.6 - - + +
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Residues in contact with THR 547 (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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543D ALA 3.0 16.6 + - - -
544D HIS* 3.1 12.9 + - - -
545D GLN 3.2 0.2 - - - -
546D ASP* 1.3 79.5 - - - +
548D GLN* 1.3 73.2 + - - +
549D ARG 3.5 3.3 + - - -
566D MET* 4.2 9.5 - - - +
567D GLU* 3.3 35.3 + - + +
570D VAL* 4.8 3.3 - - - +
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Residues in contact with GLN 548 (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* 3.1 49.0 + - - -
545D GLN* 4.6 11.4 - - - +
547D THR* 1.3 86.2 - - + +
549D ARG* 1.3 63.8 + - + +
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Residues in contact with ARG 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D GLN 4.1 16.3 + - - +
546D ASP* 5.0 7.6 - - - -
547D THR 3.4 5.6 - - - -
548D GLN* 1.3 87.0 - - + +
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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
------------------------------------------------------------
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