Contacts of the helix formed by residues 623 - 639 (chain A) in PDB entry 2KFN
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 LEU 623 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A ALA* 4.0 26.0 - - + +
573A ILE* 3.8 14.5 - - + +
574A ALA* 4.9 2.9 - - + -
578A PHE* 4.5 6.3 - - + -
586A LEU* 5.6 0.2 - - + -
589A ILE* 3.6 26.5 - - + -
590A LEU* 3.8 13.7 - - + -
593A LYS* 3.3 31.0 - - - +
622A PRO* 1.3 81.2 - - - +
624A PRO* 1.3 70.3 - - + +
626A VAL* 3.0 26.4 + - + +
627A ILE* 3.1 36.2 + - + +
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Residues in contact with PRO 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LEU* 3.9 15.5 - - + -
593A LYS* 5.4 1.1 - - - +
614A LEU* 3.5 31.8 - - + +
617A LEU* 3.5 37.9 - - + -
621A TYR* 3.7 22.0 - - + +
622A PRO 3.7 0.9 - - - -
623A LEU* 1.3 94.5 - - + +
625A LYS* 1.3 57.9 + - - +
627A ILE* 3.9 12.4 - - + +
628A LEU* 3.0 29.8 + - - +
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Residues in contact with LYS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA* 3.6 36.3 - - + +
621A TYR 3.8 10.8 - - - +
622A PRO* 3.2 16.1 + - + +
623A LEU 3.1 0.4 - - - -
624A PRO* 1.3 80.9 - - - +
626A VAL* 1.3 61.6 + - + +
628A LEU* 3.4 7.5 - - + +
629A GLU* 3.2 25.6 + - - +
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Residues in contact with VAL 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LEU* 4.1 27.0 - - + +
569A LYS* 4.9 12.3 - - + -
570A ALA* 4.1 22.7 - - + +
573A ILE* 4.4 10.3 - - + -
622A PRO* 3.3 17.0 - - + +
623A LEU* 3.0 33.5 + - + +
625A LYS* 1.3 79.6 - - + +
627A ILE* 1.3 61.5 + - + +
629A GLU* 3.7 3.7 + - - +
630A TYR* 3.0 27.5 + - - +
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Residues in contact with ILE 627 (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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578A PHE* 5.0 0.2 - - + -
580A LEU* 3.7 36.3 - - + +
586A LEU* 3.3 47.1 - - + -
590A LEU* 4.5 5.6 - - + -
614A LEU* 4.8 4.7 - - + -
623A LEU* 3.1 45.7 + - + +
624A PRO* 3.9 9.4 - - + +
626A VAL* 1.3 76.9 - - + +
628A LEU* 1.3 67.5 + - - +
630A TYR* 3.7 5.6 - - - +
631A ARG* 3.3 31.9 + - - +
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Residues in contact with LEU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A GLU* 3.5 26.2 - - - +
614A LEU* 3.5 23.8 - - + -
615A GLU* 3.5 33.7 - - + +
618A ALA* 4.5 11.0 - - + -
624A PRO 3.0 15.2 + - - +
625A LYS* 3.4 8.5 - - + +
627A ILE* 1.3 80.2 - - - +
629A GLU* 1.3 60.7 + - - +
631A ARG* 3.9 6.9 - - - +
632A GLY* 3.4 16.5 + - - -
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Residues in contact with GLU 629 (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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562A ARG* 4.2 13.5 + - - -
566A LEU* 3.4 30.3 - - + +
625A LYS 3.2 12.8 + - - +
626A VAL* 4.1 5.6 - - - +
628A LEU* 1.3 79.4 - - - +
630A TYR* 1.3 64.0 + - - +
632A GLY* 3.6 1.2 + - - -
633A LEU* 3.2 41.9 + - + +
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Residues in contact with TYR 630 (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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563A LEU* 3.1 58.4 + - + +
566A LEU* 3.8 22.1 - - + +
567A GLU* 4.4 16.3 + - + +
580A LEU* 3.7 41.7 - - + +
626A VAL 3.0 19.7 + - - +
627A ILE* 3.7 7.6 - - - +
628A LEU 3.3 0.2 - - - -
629A GLU* 1.3 76.3 - - - +
631A ARG* 1.3 68.7 + - + +
633A LEU 3.2 2.9 + - - -
634A ALA* 3.0 30.6 + - + +
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Residues in contact with ARG 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LEU* 3.3 18.4 + - + +
581A SER* 5.3 0.2 - - - +
582A SER* 3.3 39.3 + - - +
586A LEU* 3.5 16.7 - - - +
600A LYS 4.2 7.1 + - - -
602A THR* 4.2 26.7 - - - +
612A GLU* 5.2 3.2 + - - -
614A LEU* 3.5 25.4 - - - +
627A ILE* 3.3 18.8 + - + +
628A LEU* 3.9 6.7 - - - +
630A TYR* 1.3 88.8 - - + +
632A GLY* 1.3 62.8 + - - +
634A ALA* 3.2 6.8 + - - +
635A LYS* 3.0 24.4 + - - +
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Residues in contact with GLY 632 (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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628A LEU 3.4 11.4 + - - -
629A GLU* 3.6 3.3 + - - -
630A TYR 3.2 0.8 - - - -
631A ARG* 1.3 80.3 - - - +
633A LEU* 1.3 61.4 + - - +
635A LYS* 3.4 16.1 + - - +
636A LEU* 3.2 23.0 + - - +
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A LEU* 3.8 23.0 - - + +
562A ARG* 4.0 29.6 - - + +
563A LEU* 3.8 12.1 - - + +
566A LEU* 3.7 28.7 - - + -
629A GLU* 3.2 26.6 + - + +
630A TYR 3.2 5.2 + - - +
632A GLY* 1.3 72.2 - - - +
634A ALA* 1.3 65.5 + - - +
636A LEU* 3.5 7.2 + - + +
637A LYS* 3.1 24.6 + - - +
685A GLU* 3.4 35.9 - - + -
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Residues in contact with ALA 634 (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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563A LEU* 4.0 20.6 - - + +
630A TYR* 3.0 22.5 + - + +
631A ARG* 3.2 12.1 + - - +
633A LEU* 1.3 80.2 - - - +
635A LYS* 1.3 63.1 + - - +
637A LYS* 3.6 2.5 + - - +
638A SER* 3.5 19.6 + - - -
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Residues in contact with LYS 635 (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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631A ARG 3.0 13.2 + - - +
632A GLY* 3.6 17.9 - - - +
633A LEU 3.3 0.2 - - - -
634A ALA* 1.3 77.8 - - - +
636A LEU* 1.3 69.7 + - - +
638A SER* 3.7 4.1 + - - -
639A THR* 2.8 36.3 + - - +
640A TYR* 5.7 3.6 - - - -
678A ASN* 4.6 13.3 + - - +
680A PRO* 4.9 12.7 - - - +
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Residues in contact with LEU 636 (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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555A HIS* 4.5 8.7 - - + +
559A LEU* 4.7 6.7 - - + -
632A GLY 3.2 13.5 + - - +
633A LEU* 3.8 6.7 - - + +
634A ALA 3.4 0.2 - - - -
635A LYS* 1.3 89.2 - - - +
637A LYS* 1.3 60.2 + - - +
639A THR* 4.7 3.8 - - - -
640A TYR* 3.1 29.1 + - + -
641A THR* 3.4 6.2 + - - -
680A PRO* 3.7 35.0 - - + -
683A ASN* 5.5 2.0 - - - +
685A GLU* 3.4 33.4 - - + +
686A GLY 4.8 4.0 - - - +
689A ILE* 4.2 28.3 - - + -
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Residues in contact with LYS 637 (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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556A SER* 3.5 20.8 + - - +
559A LEU* 3.8 25.0 - - + +
560A THR* 3.5 24.0 + - - +
563A LEU* 4.4 15.0 - - + -
633A LEU 3.1 17.2 + - - +
634A ALA* 3.9 5.2 - - - +
635A LYS 3.3 0.2 - - - -
636A LEU* 1.3 77.2 - - - +
638A SER* 1.3 55.7 + - - +
641A THR* 3.2 17.9 + - - -
642A ASP* 2.7 61.2 + - - +
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Residues in contact with SER 638 (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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634A ALA 3.5 10.8 + - - -
635A LYS* 3.7 7.1 + - - -
636A LEU 3.5 0.2 - - - -
637A LYS* 1.3 79.3 - - - +
639A THR* 1.3 62.8 + - - +
642A ASP* 4.0 14.7 - - - +
643A LYS* 2.7 41.7 + - - +
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Residues in contact with THR 639 (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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635A LYS* 2.8 31.5 + - - +
636A LEU* 4.2 0.7 - - - -
638A SER* 1.3 83.2 + - - +
640A TYR* 1.3 95.2 + - + +
643A LYS* 3.2 20.9 - - - +
644A LEU* 5.0 0.7 - - - +
647A MET* 5.9 0.5 - - - +
678A ASN* 6.2 0.4 - - + -
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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