Contacts of the helix formed by residues 516 - 533 (chain A) in PDB entry 1GGE
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 516 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A SER 4.0 0.2 + - - -
515A GLN* 1.3 76.4 - - - +
517A PRO* 1.3 71.7 - - + +
518A PHE* 3.2 31.6 - - + -
519A GLU* 2.9 37.4 + - - +
520A GLN* 2.9 26.9 + - - +
589A SER* 4.0 0.7 - - - +
591A TYR 4.4 0.4 - - - -
592A ALA* 3.9 32.3 - - + +
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Residues in contact with PRO 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A GLN 4.6 0.7 - - - +
516A THR* 1.3 91.3 - - - +
518A PHE* 1.3 61.4 + - + +
520A GLN* 3.4 15.7 + - - +
521A ARG* 3.1 26.6 + - - +
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Residues in contact with PHE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A THR* 3.2 26.7 - - + -
517A PRO* 1.3 78.3 - - + +
519A GLU* 1.3 68.3 + - + +
521A ARG* 3.4 9.5 + - - +
522A HIS* 3.1 32.3 + + + -
591A TYR* 3.5 32.1 - + + -
742A TRP* 3.4 68.6 - + + +
745A ILE* 3.5 26.0 - - + -
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Residues in contact with GLU 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A SER* 5.2 2.5 - - - -
259A ASP* 5.2 8.5 + - + +
515A GLN* 3.4 23.9 + - + +
516A THR* 2.9 34.7 + - - +
518A PHE* 1.3 80.3 - - + +
520A GLN* 1.3 61.8 + - - +
522A HIS* 3.3 7.9 + - - +
523A ILE* 3.0 29.2 + - + +
589A SER* 2.7 21.9 + - - -
590A LEU* 2.8 40.8 + - + +
591A TYR* 3.9 21.5 - - + -
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Residues in contact with GLN 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A TRP* 2.8 74.3 + - + +
513A LEU* 4.1 8.1 + - - +
515A GLN* 3.7 16.4 + - + -
516A THR 2.9 13.0 + - - +
517A PRO* 3.5 15.9 - - - +
518A PHE 3.2 0.2 - - - -
519A GLU* 1.3 74.9 - - - +
521A ARG* 1.3 59.7 + - - +
523A ILE* 3.1 7.0 + - - +
524A VAL* 2.9 30.1 + - - +
553A THR* 6.1 0.2 - - - +
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Residues in contact with ARG 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A PRO 3.1 13.3 + - - +
518A PHE* 3.7 8.9 - - - +
519A GLU 3.3 0.2 - - - -
520A GLN* 1.3 77.2 - - - +
522A HIS* 1.3 72.5 + - - +
524A VAL* 3.0 10.7 + - + +
525A ASP* 2.8 47.2 + - - +
745A ILE* 3.5 36.1 - - - +
746A PRO* 5.2 8.5 - - - +
749A ASP* 5.2 6.5 + - - -
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Residues in contact with HIS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 4.9 3.1 + - - -
257A MET 3.5 7.2 - - - +
259A ASP* 2.7 42.0 + - - +
303A VAL* 4.1 24.2 - - + +
304A TRP 6.3 0.2 - - - -
518A PHE* 3.1 19.8 + + - -
519A GLU* 3.3 7.8 + - - +
521A ARG* 1.3 89.7 - - + +
523A ILE* 1.3 57.7 + - - +
525A ASP* 3.4 11.7 + - + +
526A GLY* 2.9 23.0 + - - -
692A LEU* 4.7 2.1 - - + +
742A TRP* 4.1 16.2 - + - -
745A ILE* 3.9 21.7 - - + +
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Residues in contact with ILE 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A MET* 4.2 9.6 - - + +
257A MET* 3.6 12.1 - - + +
258A SER* 3.4 24.0 - - - +
511A PHE* 3.8 28.9 - - + -
512A TRP* 4.1 24.2 - - + -
515A GLN* 3.9 17.0 - - + +
519A GLU* 3.0 19.6 + - + +
520A GLN* 3.4 7.2 - - - +
522A HIS* 1.3 71.7 - - - +
524A VAL* 1.3 68.2 + - - +
526A GLY* 3.1 1.4 + - - -
527A PHE* 3.0 48.8 + - + -
554A LEU* 4.3 1.6 - - + -
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Residues in contact with VAL 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A TRP* 3.9 19.3 - - + -
520A GLN 2.9 17.1 + - - +
521A ARG* 3.3 11.4 - - + +
523A ILE* 1.3 78.5 - - - +
525A ASP* 1.3 62.5 + - - +
527A PHE* 3.4 2.8 + - - +
528A SER* 2.8 33.3 + - - +
554A LEU* 4.0 11.0 - - + +
557A ALA* 3.7 36.1 - - + -
558A VAL* 4.1 8.0 - - + +
561A ASN* 3.7 22.4 - - - +
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Residues in contact with ASP 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A TRP* 6.3 3.1 - - + -
521A ARG* 2.8 43.0 + - - +
522A HIS* 3.7 13.6 - - + +
524A VAL* 1.3 79.6 - - - +
526A GLY* 1.3 57.6 + - - +
528A SER* 3.7 5.7 - - - -
529A PHE* 2.9 33.5 + - - +
561A ASN* 4.3 7.3 + - - -
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Residues in contact with GLY 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 4.0 23.3 - - - +
257A MET* 3.8 14.4 - - - -
304A TRP* 6.3 0.9 - - - -
522A HIS 2.9 16.6 + - - -
523A ILE 3.1 3.3 + - - -
525A ASP* 1.3 73.6 - - - +
527A PHE* 1.3 64.3 + - - +
529A PHE* 3.7 3.6 - - - +
530A GLU* 3.0 28.2 + - - +
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Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TRP* 3.6 34.8 - + - -
250A LEU* 5.6 2.7 - - + -
253A VAL* 3.6 18.8 - - + -
254A MET* 3.7 28.9 - - - -
257A MET* 3.9 16.3 - - + -
523A ILE* 3.0 36.6 + - + -
524A VAL 3.8 5.6 - - - +
526A GLY* 1.3 73.1 - - - +
528A SER* 1.3 58.2 + - - +
530A GLU* 4.6 1.3 - - - -
531A LEU* 2.9 39.1 + - + +
543A VAL* 4.6 5.2 - - + -
547A LEU* 3.6 35.9 - - + -
554A LEU* 4.5 10.8 - - + -
558A VAL* 3.9 15.7 - - + -
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Residues in contact with SER 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A VAL 2.8 22.8 + - - -
525A ASP* 3.7 5.6 - - - -
527A PHE* 1.3 77.4 - - - +
529A PHE* 1.3 61.6 + - - +
532A SER* 3.0 25.6 + - - -
558A VAL* 3.8 13.6 - - - -
561A ASN* 2.8 42.6 + - - +
562A LEU* 3.7 12.6 - - - +
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Residues in contact with PHE 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 6.0 1.8 - - - -
233A GLN* 5.9 2.0 - - - -
235A ALA* 4.6 8.7 - - + -
304A TRP* 3.5 48.5 - + + +
308A GLN* 3.9 19.5 - - - -
525A ASP 2.9 21.6 + - - +
526A GLY* 3.7 4.0 - - - +
528A SER* 1.3 71.3 - - - +
530A GLU* 1.3 76.5 + - + +
532A SER* 2.6 25.3 + - - -
533A LYS* 3.5 43.5 + - + +
653D THR* 5.6 2.0 - - - -
655D ALA* 4.5 9.6 - - + -
656D GLY* 4.0 17.3 - - - -
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Residues in contact with GLU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 3.5 23.8 + - - +
233A GLN* 5.6 0.5 - - - +
234A SER* 2.7 31.0 + - - -
235A ALA* 3.2 30.3 + - + +
240A TRP* 3.1 35.0 + - + +
257A MET* 3.7 13.9 - - - -
304A TRP* 5.7 2.6 - - - -
526A GLY 3.0 21.7 + - - +
527A PHE 3.9 1.1 - - - +
529A PHE* 1.3 83.6 - - + +
531A LEU* 1.3 58.1 + - - +
533A LYS* 3.0 24.4 + - - +
534A VAL* 3.6 7.8 + - - +
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Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A TRP* 3.6 46.7 - - + -
527A PHE* 2.9 29.2 + - + +
530A GLU* 1.3 72.0 - - - +
532A SER* 1.3 57.1 + - - +
534A VAL* 3.0 23.6 + - + +
540A ARG* 3.2 34.0 + - + +
543A VAL* 3.8 31.0 - - + -
544A VAL* 4.6 2.0 - - + -
547A LEU* 5.2 0.4 - - + -
558A VAL* 4.2 11.9 - - + -
562A LEU* 3.8 31.2 - - + -
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Residues in contact with SER 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A SER 3.0 16.3 + - - -
529A PHE* 2.6 22.8 + - - -
531A LEU* 1.3 75.6 - - - +
533A LYS* 1.3 69.5 + - - +
534A VAL 3.3 1.8 + - - -
540A ARG* 4.2 5.5 + - - +
562A LEU* 4.0 2.8 - - - +
637D MET* 3.5 49.8 - - - +
651D ALA 4.5 4.2 - - - +
652D ALA* 5.4 1.7 - - - +
653D THR* 5.0 12.4 + - - -
656D GLY* 5.3 1.2 - - - -
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Residues in contact with LYS 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLN* 5.8 1.8 + - - -
235A ALA* 3.6 31.3 - - + +
236A HIS* 4.3 3.3 - - - -
237A ASP* 3.8 4.2 - - - +
308A GLN* 5.4 1.4 - - - +
529A PHE* 3.5 42.3 - - + +
530A GLU 3.0 10.8 + - - +
532A SER* 1.3 83.2 - - - +
534A VAL* 1.3 63.0 + - - +
535A VAL* 3.5 10.7 + - - +
313D ARG 5.1 8.1 + - - -
652D ALA* 6.0 4.0 - - + -
656D GLY* 2.8 35.4 + - - -
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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