Contacts of the helix formed by residues 529 - 544 (chain A) in PDB entry 1KLN
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 ILE 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524A ASN* 5.9 0.7 - - - +
525A VAL* 2.8 31.4 + - + +
527A GLU 3.8 0.4 - - - -
528A ASN* 1.3 81.6 - - + +
530A GLU* 1.3 81.7 + - - +
531A MET 3.4 1.2 + - - -
532A PRO* 3.4 4.0 - - - +
533A LEU* 3.1 24.7 + - - +
819A ASP* 4.0 15.9 - - - +
821A ARG* 4.3 1.3 - - - +
854A ASP* 3.7 39.9 - - + +
857A LYS* 3.6 33.4 - - + -
858A ARG* 4.2 15.3 - - + +
861A ILE* 3.6 7.3 - - + +
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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
----------------------------------------------------------
444A LEU* 3.6 21.2 - - + +
447A TYR* 3.4 9.2 - - - -
448A ILE* 3.7 16.2 - - + -
525A VAL* 3.0 12.5 + - - +
526A PHE* 3.8 12.6 - - + +
529A ILE* 1.3 87.6 - - - +
531A MET* 1.3 64.5 + - - +
533A LEU* 3.4 4.3 + - - +
534A VAL 3.6 2.6 + - - -
661A GLN* 2.9 34.6 + - - +
821A ARG* 2.9 44.6 + - - -
857A LYS* 2.9 19.6 + - - -
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Residues in contact with MET 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 5.0 0.2 - - + -
438A ILE* 3.9 30.9 - - + +
439A ALA* 3.3 19.1 - - - +
440A PHE 4.3 1.6 - - - -
441A ASP* 3.3 39.5 - - + +
444A LEU* 4.0 5.2 - - - -
526A PHE* 3.0 55.4 + - + +
527A GLU* 4.7 2.9 - - - +
530A GLU* 1.3 75.1 - - - +
532A PRO* 1.4 66.4 - - + +
533A LEU 2.9 1.9 + - - -
534A VAL* 2.9 35.9 + - + +
535A PRO* 3.8 2.6 - - - +
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Residues in contact with PRO 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU 3.5 15.7 - - - +
528A ASN* 3.7 22.0 - - - +
529A ILE 3.4 13.7 - - - +
531A MET* 1.4 91.2 - - + +
533A LEU* 1.3 59.1 + - - +
534A VAL 3.3 0.2 - - - -
535A PRO* 3.5 17.7 - - + +
536A VAL* 3.7 10.0 - - - +
861A ILE* 3.9 22.3 - - + +
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Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ILE 3.1 17.4 + - - +
530A GLU 3.5 4.3 - - - +
531A MET 2.9 1.4 + - - -
532A PRO* 1.3 76.4 - - - +
534A VAL* 1.3 56.3 + - - +
536A VAL* 2.7 55.7 + - + +
537A LEU* 3.0 13.1 + - + -
661A GLN* 3.5 24.2 - - + +
669A LEU* 4.7 6.7 - - + -
857A LYS* 3.4 58.6 - - + +
860A MET* 3.9 13.5 - - + -
861A ILE* 3.9 7.8 - - + +
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU 4.0 4.0 - - - +
422A LYS* 3.7 37.6 - - + +
438A ILE* 3.9 19.7 - - + -
441A ASP* 4.1 9.6 - - - +
444A LEU* 3.8 23.6 - - + -
531A MET* 2.9 21.0 + - + +
533A LEU* 1.3 74.9 - - - +
535A PRO* 1.3 69.8 - - + +
537A LEU* 3.1 14.3 + - - +
538A SER 3.2 8.8 + - - -
661A GLN* 3.7 19.2 + - - +
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Residues in contact with PRO 535 (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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425A ARG* 4.2 21.0 - - + +
434A GLU* 5.5 1.8 - - - +
435A LEU 5.7 0.2 - - - +
438A ILE* 4.2 26.5 - - + -
531A MET 3.8 4.7 - - - +
532A PRO* 3.5 16.2 - - + +
534A VAL* 1.3 98.1 - - + +
536A VAL* 1.3 61.7 + - + +
538A SER* 3.3 2.7 + - - +
539A ARG* 3.1 42.0 + - - +
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Residues in contact with VAL 536 (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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532A PRO 3.7 14.6 - - - +
533A LEU* 2.7 48.6 + - + +
535A PRO* 1.3 69.9 - - - +
537A LEU* 1.3 70.2 + - + +
539A ARG* 3.1 5.6 + - - +
540A ILE* 3.0 29.1 + - + +
860A MET* 4.6 10.5 - - + -
861A ILE* 4.5 10.8 - - + -
864A ASP* 3.5 45.5 - - + +
876A MET* 4.5 6.9 - - + +
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Residues in contact with LEU 537 (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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422A LYS* 3.5 19.1 - - + +
533A LEU* 3.0 16.2 + - + +
534A VAL* 3.1 6.0 + - - +
536A VAL* 1.3 82.9 - - + +
538A SER* 1.3 61.6 + - - +
540A ILE* 3.5 16.8 + - + +
541A GLU* 3.2 28.6 + - - +
659A TYR* 3.9 46.7 - - + +
661A GLN* 3.7 35.2 - - + +
669A LEU* 4.3 19.7 - - + -
860A MET* 5.1 2.0 - - - -
879A GLN* 6.5 0.2 - - + -
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Residues in contact with SER 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASN* 3.5 14.9 + - - -
422A LYS* 2.9 35.2 + - - +
425A ARG* 3.5 30.1 - - - -
426A GLY 3.6 3.8 + - - -
534A VAL 3.2 9.5 + - - -
535A PRO 3.3 2.0 + - - -
536A VAL 3.2 0.4 - - - -
537A LEU* 1.3 76.4 - - - +
539A ARG* 1.3 62.6 + - - +
541A GLU* 3.9 3.0 + - - +
542A ARG* 3.2 30.3 + - - +
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Residues in contact with ARG 539 (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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425A ARG* 3.9 21.1 - - - +
434A GLU* 3.1 24.4 + - - -
535A PRO* 3.1 36.1 + - - +
536A VAL* 3.1 8.1 + - - +
538A SER* 1.3 75.7 - - - +
540A ILE* 1.3 66.5 + - + +
542A ARG* 3.2 4.6 + - - +
543A ASN* 3.0 34.1 + - - +
864A ASP* 2.8 40.6 + - - +
868A GLN* 3.0 41.1 + - - +
876A MET* 6.2 0.7 - - + -
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Residues in contact with ILE 540 (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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536A VAL* 3.0 20.0 + - + +
537A LEU* 4.1 13.9 - - + +
539A ARG* 1.3 73.8 - - + +
541A GLU* 1.3 64.1 + - - +
543A ASN* 3.0 3.5 + - - +
544A GLY* 2.9 21.1 + - - -
657A THR* 5.7 0.4 - - + +
659A TYR* 3.8 25.1 - - + -
860A MET* 4.3 18.8 - - - -
876A MET* 3.5 55.4 - - + +
877A ILE 3.8 24.5 - - - +
878A MET* 4.2 3.6 - - - -
879A GLN* 5.0 7.2 - - + -
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Residues in contact with GLU 541 (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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363A ASN* 5.0 9.1 + - - +
422A LYS* 2.7 41.9 + - - +
537A LEU 3.2 15.8 + - - +
538A SER* 4.4 4.0 - - - +
540A ILE* 1.3 77.3 - - - +
542A ARG* 1.3 61.8 + - + +
543A ASN 3.3 0.3 + - - -
544A GLY* 3.5 3.5 + - - -
656A HIS* 2.7 32.5 + - + +
657A THR* 3.5 22.9 - - - +
658A SER* 3.7 4.2 - - - -
659A TYR* 2.9 34.6 + - + +
12B G 4.4 2.8 + - - -
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Residues in contact with ARG 542 (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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363A ASN* 2.7 52.3 + - + +
364A ILE* 3.9 20.3 - - + +
425A ARG* 4.2 10.4 - - - +
426A GLY* 3.0 27.8 + - - -
429A ALA* 3.8 12.7 + - - +
430A ASN* 3.0 22.8 + - - +
538A SER* 3.2 26.2 + - - +
539A ARG* 3.2 5.4 + - - +
541A GLU* 1.3 76.1 - - + +
543A ASN* 1.3 69.2 + - - +
652A THR* 5.2 3.1 - - - +
656A HIS* 3.6 12.5 - - - -
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Residues in contact with ASN 543 (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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539A ARG* 3.0 21.4 + - - +
540A ILE 3.0 7.9 + - - +
542A ARG* 1.3 81.5 + - - +
544A GLY* 1.3 70.7 + - - +
654A ARG* 3.5 17.2 + - - -
656A HIS* 3.3 14.1 - - - -
875A ARG* 3.7 45.9 + - - +
876A MET 3.7 17.5 + - - +
877A ILE* 4.7 2.2 - - + -
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Residues in contact with GLY 544 (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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540A ILE 2.9 13.0 + - - -
541A GLU* 3.5 5.3 + - - -
543A ASN* 1.3 80.8 - - - +
545A VAL* 1.3 61.3 - - - -
654A ARG* 3.0 12.4 + - - -
655A VAL 3.1 13.5 - - - -
656A HIS* 3.6 9.4 - - - -
657A THR* 5.0 4.9 - - - -
877A ILE* 3.3 26.4 + - - +
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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