Contacts of the helix formed by residues 521 - 538 (chain D) in PDB entry 3F7F
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 521 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D LEU* 1.3 75.6 - - - +
522D ASN* 1.3 66.2 + - - +
523D ASP* 3.7 7.8 + - - +
524D VAL* 3.1 30.6 + - - +
525D LEU* 2.9 27.3 + - - +
561D GLN 5.6 0.2 + - - -
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Residues in contact with ASN 522 (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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394D ASP* 3.2 49.9 + - - +
395D LEU* 4.5 1.9 - - - +
396D ASP 3.6 24.9 + - - +
397D ILE* 4.8 6.5 - - + +
521D SER* 1.3 74.6 - - - +
523D ASP* 1.3 63.7 + - - +
524D VAL 3.2 0.2 + - - -
525D LEU* 3.2 10.9 + - - +
526D ARG* 2.8 45.5 + - + +
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Residues in contact with ASP 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D SER* 3.3 7.6 + - - +
522D ASN* 1.3 79.2 - - - +
524D VAL* 1.3 61.9 + - + +
526D ARG* 3.9 15.0 - - - +
527D SER* 3.2 23.6 + - - -
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Residues in contact with VAL 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520D LEU* 4.5 9.6 - - + -
521D SER* 3.1 29.7 + - - +
523D ASP* 1.3 76.4 - - + +
525D LEU* 1.3 64.8 + - - +
527D SER* 2.6 23.1 + - - -
528D ILE* 3.1 24.5 + - + +
557D CYS 3.7 20.0 - - - +
558D LEU* 4.1 9.6 - - + -
561D GLN* 3.8 35.9 - - + +
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Residues in contact with LEU 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D ILE* 3.5 27.6 - - + -
517D ALA* 4.0 22.9 - - + +
518D SER* 5.9 0.4 - - - -
520D LEU* 4.0 29.2 - - + +
521D SER 2.9 23.7 + - - +
522D ASN* 3.8 7.4 - - - +
524D VAL* 1.3 76.6 - - - +
526D ARG* 1.3 57.0 + - - +
528D ILE* 3.1 12.1 + - + +
529D SER* 2.9 28.4 + - - -
631D LEU* 4.2 19.9 - - + +
632D GLN* 6.3 0.7 - - + -
635D LEU* 4.9 8.7 - - + -
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Residues in contact with ARG 526 (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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396D ASP 3.3 10.1 + - - -
397D ILE* 3.0 61.0 + - + +
398D VAL 3.8 2.2 + - - -
399D THR 2.5 32.1 + - - -
400D LYS* 4.3 3.2 - - - +
401D THR* 3.8 25.5 + - - +
522D ASN* 2.8 40.3 + - - +
523D ASP* 3.9 15.0 - - - +
525D LEU* 1.3 72.3 - - - +
527D SER* 1.3 58.1 + - - +
529D SER* 3.3 2.9 + - - -
530D LYS* 2.9 29.8 + - - +
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Residues in contact with SER 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D ASP 3.2 12.0 + - - -
524D VAL* 2.6 24.7 + - - -
526D ARG* 1.3 80.3 - - - +
528D ILE* 1.3 56.1 + - - +
530D LYS* 3.7 7.6 + - - +
531D LYS* 3.2 29.3 + - - +
556D ASN 5.7 0.4 - - - -
557D CYS* 3.4 26.8 + - - +
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Residues in contact with ILE 528 (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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520D LEU* 4.8 3.6 - - + -
524D VAL* 3.1 19.7 + - + +
525D LEU* 3.1 15.0 + - + +
527D SER* 1.3 77.2 + - - +
529D SER* 1.3 64.6 + - - +
530D LYS 3.2 0.2 - - - -
531D LYS* 3.1 6.7 + - - +
532D PHE* 3.0 52.8 + - + -
553D ILE* 4.5 6.1 - - + -
557D CYS* 3.6 19.7 - - + -
558D LEU* 3.3 43.3 - - + -
631D LEU* 4.3 6.7 - - + -
635D LEU* 4.1 13.0 - - + -
638D VAL* 6.2 0.2 - - + -
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Residues in contact with SER 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D ILE* 4.8 1.6 - - - -
525D LEU 2.9 12.7 + - - -
526D ARG* 3.6 11.0 - - - -
528D ILE* 1.3 75.7 - - - +
530D LYS* 1.3 64.7 + - - +
532D PHE* 3.0 10.6 + - - -
533D LEU* 3.0 12.2 + - - +
627D TYR* 2.5 29.4 + - - -
631D LEU* 3.8 16.4 - - - -
658D HIS* 2.8 28.3 + - - -
662D PHE* 4.1 9.7 - - - -
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Residues in contact with LYS 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D ARG 2.9 17.7 + - - +
527D SER* 3.7 9.0 - - - +
528D ILE 3.2 0.2 - - - -
529D SER* 1.3 77.1 - - - +
531D LYS* 1.3 57.9 + - + +
533D LEU* 3.1 22.9 + - + +
534D ASP* 3.0 55.1 + - - +
539D GLU* 3.3 25.0 + - - -
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Residues in contact with LYS 531 (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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527D SER 3.2 15.1 + - - +
528D ILE 3.1 10.0 + - - +
530D LYS* 1.3 80.5 - - + +
532D PHE* 1.3 63.8 + - - +
534D ASP* 3.0 27.2 + - - +
535D ILE* 3.1 10.2 + - - +
540D LEU* 3.6 28.2 - - + +
552D ASP* 3.3 25.1 + - - -
553D ILE* 3.3 27.6 - - + +
556D ASN* 4.1 20.4 - - - +
557D CYS* 3.8 12.1 - - - -
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Residues in contact with PHE 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528D ILE* 3.0 39.4 + - + -
529D SER* 3.0 7.4 + - - +
531D LYS* 1.3 76.7 - - - +
533D LEU* 1.3 61.0 + - - +
535D ILE* 3.3 20.7 + - + +
536D ILE* 3.5 10.9 + - - +
550D PHE* 4.9 3.6 - + - -
553D ILE* 3.4 28.7 - - + -
631D LEU* 3.6 25.4 - - + -
634D LEU* 3.5 39.5 - - + -
635D LEU* 4.3 2.0 - - - -
638D VAL* 3.8 23.3 - - + -
655D LEU* 3.6 27.5 - - + +
658D HIS* 3.6 14.2 + - + +
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Residues in contact with LEU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D SER 3.0 16.4 + - - +
530D LYS* 3.1 24.0 + - + +
532D PHE* 1.3 74.7 - - - +
534D ASP* 1.3 62.5 + - - +
536D ILE* 3.1 4.2 + - - +
537D THR* 2.8 34.3 + - + +
658D HIS* 4.0 11.4 - - + +
659D TYR* 3.4 45.0 - - + +
662D PHE* 3.5 43.3 - - + -
729D ILE* 3.8 17.7 - - + -
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Residues in contact with ASP 534 (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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530D LYS* 3.0 50.2 + - - +
531D LYS* 3.0 27.5 + - - +
533D LEU* 1.3 74.5 - - - +
535D ILE* 1.3 57.6 + - - +
537D THR* 3.1 7.1 + - - -
538D GLY 2.7 27.7 + - - -
539D GLU* 3.1 41.9 + - + +
540D LEU* 3.3 18.0 + - + -
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Residues in contact with ILE 535 (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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531D LYS 3.1 10.3 + - - +
532D PHE* 3.5 7.9 - - + +
533D LEU 3.2 0.2 - - - -
534D ASP* 1.3 79.6 - - - +
536D ILE* 1.3 66.0 + - + +
538D GLY* 3.7 6.8 + - - -
540D LEU* 3.8 22.5 - - + +
549D LYS* 4.0 41.5 + - + +
550D PHE* 4.2 10.3 - - + -
553D ILE* 4.2 22.2 - - + -
655D LEU* 4.1 36.1 - - + -
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Residues in contact with ILE 536 (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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532D PHE 3.5 10.0 + - - +
533D LEU 3.1 7.6 + - - +
535D ILE* 1.3 82.8 - - + +
537D THR* 1.3 61.3 + - - +
538D GLY* 3.6 0.3 + - - -
652D SER 5.5 0.7 - - - +
655D LEU* 3.6 40.4 - - + +
656D ASP* 4.4 11.0 - - + +
659D TYR* 3.6 34.8 - - + -
714D ILE* 4.1 15.5 - - + -
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Residues in contact with THR 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 LEU* 2.8 23.7 + - + +
534D ASP* 3.1 18.7 + - - -
536D ILE* 1.3 76.4 - - - +
538D GLY* 1.3 59.9 + - - +
539D GLU* 3.8 11.8 + - - +
659D TYR* 3.9 19.3 - - + +
725D ARG* 3.5 46.2 + - - +
729D ILE* 5.1 5.4 - - + -
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Residues in contact with GLY 538 (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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534D ASP 2.7 14.8 + - - -
535D ILE 3.7 3.8 + - - -
536D ILE 3.3 3.0 - - - -
537D THR* 1.3 76.5 - - - +
539D GLU* 1.3 59.2 + - - -
540D LEU 2.8 15.2 + - - -
541D PRO* 3.2 17.4 - - - +
542D ASP* 5.2 4.3 - - - -
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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