Contacts of the helix formed by residues 514 - 523 (chain A) in PDB entry 3GKL
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 SER 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A GLN 4.3 0.8 + - - -
513A PHE* 1.3 74.2 - - - +
515A ARG* 1.3 57.5 + - - +
516A ASN* 3.6 3.2 + - - +
517A ASN* 2.9 32.1 + - - +
518A ASN* 2.9 13.9 + - - +
507B PRO* 4.5 4.9 - - - -
1053C ILE 5.3 0.4 - - - -
1054C TYR* 3.1 35.2 + - - -
1056C PRO* 4.0 15.5 - - - -
1062C ASP* 5.2 1.3 - - - -
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Residues in contact with ARG 515 (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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513A PHE 4.0 0.2 + - - -
514A SER* 1.3 71.3 - - - +
516A ASN* 1.3 82.7 + - - +
518A ASN* 3.2 2.6 + - - +
519A ASP* 3.0 41.3 + - - +
483B LYS* 3.7 28.7 - - - +
487B LYS* 4.2 10.7 - - - +
502B GLU* 2.9 37.6 + - - +
505B LYS* 3.5 44.0 - - + +
506B ASP* 4.9 3.1 - - + +
507B PRO* 4.0 9.6 - - + +
1023C CYS* 3.2 26.5 + - - +
1024C ASP* 5.6 2.6 + - - -
1062C ASP* 3.8 17.3 + - - +
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Residues in contact with ASN 516 (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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514A SER* 3.4 2.3 + - - +
515A ARG* 1.3 103.2 - - - +
517A ASN* 1.3 61.4 + - - +
519A ASP* 3.5 4.6 + - - +
520A ARG* 3.4 24.9 + - - +
1023C CYS* 3.2 31.1 + - - +
1053C ILE* 2.6 35.5 - - + +
1054C TYR* 3.6 19.6 - - + -
1062C ASP* 3.8 25.9 + - - +
1064C PRO* 6.1 0.2 - - - +
1067C ILE* 5.0 0.5 - - - +
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Residues in contact with ASN 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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513A PHE* 4.2 16.2 - - + -
514A SER* 2.9 19.1 + - - +
516A ASN* 1.3 74.8 - - - +
518A ASN* 1.3 63.9 + - - +
520A ARG* 3.1 17.8 + - - +
521A MET* 3.2 20.1 + - - +
527A PRO* 3.4 20.5 - - + +
528A LYS* 3.2 40.2 + - - +
1054C TYR* 3.5 30.9 + - - +
1055C TYR* 3.8 8.5 + - - -
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Residues in contact with ASN 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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504A SER* 4.1 9.1 - - - +
510A SER* 3.3 35.1 + - - +
513A PHE* 2.7 26.0 - - - +
514A SER 2.9 15.8 + - - +
515A ARG 3.9 0.7 - - - +
517A ASN* 1.3 72.2 - - - +
519A ASP* 1.3 56.9 - - - +
521A MET* 3.3 25.0 + - - +
522A LYS* 2.9 36.8 + - + +
504B SER 5.1 2.0 - - - +
505B LYS* 3.4 34.5 - - - +
507B PRO* 4.0 2.4 - - - +
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Residues in contact with ASP 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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515A ARG* 3.0 38.7 + - - +
516A ASN* 3.6 7.4 - - - +
517A ASN 3.1 0.2 - - - -
518A ASN* 1.3 73.5 - - - +
520A ARG* 1.3 66.9 + - - +
522A LYS* 3.6 9.0 + - - +
523A VAL* 3.9 6.2 - - - +
505B LYS* 3.2 30.8 + - + +
1023C CYS 3.2 21.1 - - - +
1024C ASP* 4.0 4.4 - - - +
1025C ALA* 3.2 30.3 + - - +
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Residues in contact with ARG 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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516A ASN* 3.4 13.3 + - - +
517A ASN* 3.1 19.2 + - - +
519A ASP* 1.3 77.9 + - - +
521A MET* 1.3 58.1 + - - +
523A VAL* 2.9 28.1 + - - +
525A LYS* 3.1 42.9 + - + +
526A ALA 4.2 13.7 - - - +
528A LYS* 4.4 8.0 - - - +
1022C ILE 3.1 21.2 + - - -
1023C CYS* 4.9 4.0 - - - +
1025C ALA* 3.4 40.3 + - - +
1028C THR* 5.3 2.6 + - - -
1030C GLU* 4.5 6.3 + - - -
1033C LEU* 3.7 21.6 - - - +
1054C TYR* 3.0 37.5 + - - -
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Residues in contact with MET 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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500A TRP* 3.7 37.0 - - + +
501A GLU* 3.0 27.5 + - - -
503A VAL* 3.9 15.5 - - + -
504A SER* 3.9 9.9 - - - -
513A PHE* 3.3 43.7 - - + -
517A ASN 3.2 15.6 + - - +
518A ASN* 3.5 20.0 - - - +
520A ARG* 1.3 79.7 - - - +
522A LYS* 1.3 61.4 + - - +
523A VAL 3.3 0.2 - - - -
524A GLY 3.3 4.6 + - - +
525A LYS 3.2 16.2 - - - +
527A PRO* 3.7 18.8 - - + -
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Residues in contact with LYS 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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501A GLU* 3.4 16.4 - - - +
504A SER* 3.4 33.3 + - - +
505A LYS* 4.5 9.6 - - - +
518A ASN* 2.9 23.1 + - - +
519A ASP* 3.9 8.3 - - - +
520A ARG 3.0 0.6 - - - -
521A MET* 1.3 78.1 - - - +
523A VAL* 1.3 62.5 + - + +
524A GLY 3.4 0.4 - - - -
504B SER* 3.3 39.8 + - - +
505B LYS* 4.3 16.7 - - + +
518B ASN* 4.5 3.5 + - - +
522B LYS* 3.4 56.5 - - + +
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Residues in contact with VAL 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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497A LYS* 4.5 9.4 + - - +
501A GLU* 4.3 7.0 - - - -
519A ASP 3.9 10.8 - - - +
520A ARG 3.1 12.3 - - - +
522A LYS* 1.3 78.9 - - + +
524A GLY* 1.3 59.3 + - - +
525A LYS* 3.5 25.2 + - + +
1025C ALA* 4.1 14.8 - - + +
1026C ASP* 4.6 22.7 - - + +
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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