Contacts of the helix formed by residues 2 - 17 (chain L) in PDB entry 1KFX
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 ALA 2 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3L GLY* 1.3 70.1 + - - +
5L ALA* 4.4 3.1 + - - +
6L ALA* 3.1 20.9 + - - +
850S VAL 4.5 1.1 - - - -
851S MET* 2.9 27.9 - - + +
853S SER* 2.6 19.7 - - - +
863S GLU* 4.4 17.7 - - + +
941S ARG* 5.2 9.8 - - - +
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Residues in contact with GLY 3 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L ALA* 1.3 91.5 - - - +
4L ILE* 1.3 70.4 + - - -
5L ALA* 3.0 4.3 - - - -
6L ALA* 2.8 7.1 + - - +
7L LYS 3.7 1.0 + - - -
850S VAL 3.3 24.7 + - - -
851S MET 3.5 5.5 + - - -
852S ASP 3.5 11.0 - - - -
853S SER* 2.6 14.4 + - - -
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Residues in contact with ILE 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L GLY* 1.3 75.3 - - - -
5L ALA* 1.3 65.7 + - + +
6L ALA 3.0 0.3 + - - -
7L LYS* 3.1 11.8 + - + +
8L LEU* 2.8 34.0 + - + +
645L VAL* 5.5 1.8 - - + -
849S ALA 3.7 12.8 - - - +
850S VAL* 4.9 3.4 - - - -
852S ASP 3.3 7.0 + - - +
853S SER* 4.7 0.9 - - - +
855S THR* 4.3 13.9 - - - +
963S GLN* 4.3 17.9 - - + +
964S LEU* 4.1 28.9 - - + +
967S TYR* 3.7 47.6 - - + +
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Residues in contact with ALA 5 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L ALA 4.5 2.7 - - - +
3L GLY* 2.8 3.6 + - - +
4L ILE* 1.3 83.9 - - + +
6L ALA* 1.3 57.6 + - - +
8L LEU* 3.3 6.6 + - - +
9L ALA* 2.8 30.9 + - - +
942S ALA* 3.4 44.9 - - + +
945S SER* 4.2 9.8 - - - +
946S LEU* 4.0 5.6 - - + +
964S LEU* 4.3 9.6 - - + -
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Residues in contact with ALA 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L ALA* 3.1 27.7 + - - +
3L GLY 2.8 9.0 + - - +
5L ALA* 1.3 69.4 - - - +
7L LYS* 1.3 55.3 + - - +
8L LEU 2.5 16.7 + - - -
9L ALA* 2.7 16.0 + - - +
10L LYS* 3.0 14.3 + - - +
853S SER* 3.9 5.6 - - - +
945S SER* 4.9 6.7 + - - +
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Residues in contact with LYS 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L GLY 3.7 0.8 + - - -
4L ILE* 3.1 10.6 + - + +
6L ALA* 1.3 76.4 - - - +
8L LEU* 1.3 57.3 + - - +
10L LYS* 4.4 17.3 - - - +
11L ASP* 3.2 36.6 + - - +
641L GLN* 6.2 2.5 - - - +
853S SER* 2.9 36.4 - - - +
854S ASP* 4.8 7.2 - - - +
855S THR* 5.9 2.0 - - - +
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Residues in contact with LEU 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L ILE* 2.8 20.6 + - + +
5L ALA* 3.4 5.2 - - - +
6L ALA 2.5 10.5 + - - -
7L LYS* 1.3 76.4 - - - +
9L ALA* 1.3 59.7 + - - +
10L LYS 3.2 1.6 - - - -
11L ASP* 3.5 22.9 - - + +
12L ARG* 3.5 15.4 + - - +
946S LEU* 4.7 8.5 - - + +
960S GLU* 3.9 48.9 - - + +
963S GLN* 3.3 28.7 - - + +
964S LEU* 4.1 21.1 - - + -
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Residues in contact with ALA 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ALA 2.8 15.4 + - - +
6L ALA* 2.7 5.8 + - - +
8L LEU* 1.3 75.6 - - - +
10L LYS* 1.3 63.9 + - - +
11L ASP 3.1 2.0 - - - -
12L ARG* 3.3 20.3 - - - +
13L GLU* 3.0 24.9 - - + +
945S SER* 4.2 18.8 - - - +
946S LEU* 4.2 12.3 - - + -
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Residues in contact with LYS 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ALA 3.0 15.1 + - - +
7L LYS* 4.7 14.5 - - - +
9L ALA* 1.3 77.7 - - - +
11L ASP* 1.3 61.5 + - - +
12L ARG 3.5 0.2 - - - -
13L GLU* 3.6 7.1 - - - -
14L ALA* 2.7 42.0 + - + +
18L LEU* 4.1 20.6 - - + -
25L ILE* 4.4 9.5 - - - +
148L GLU* 3.3 30.9 + - - -
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Residues in contact with ASP 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L LYS* 3.2 43.1 + - - +
8L LEU* 3.5 21.1 - - + +
9L ALA 3.1 0.6 - - - -
10L LYS* 1.3 80.9 - - - +
12L ARG* 1.3 60.7 + - + +
13L GLU 3.1 0.9 - - - -
14L ALA* 3.7 5.0 - - - +
15L ALA* 2.8 32.7 + - - +
960S GLU* 6.0 0.7 - - - +
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Residues in contact with ARG 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LEU 3.5 9.2 - - - +
9L ALA* 3.3 29.8 - - - +
11L ASP* 1.3 74.2 - - - +
13L GLU* 1.3 66.3 + - + +
15L ALA* 3.4 7.3 + - - +
16L GLU* 3.2 26.0 + - - +
946S LEU* 3.6 42.6 + - - +
955S GLN 2.9 24.2 + - - +
956S VAL* 4.8 0.2 - - - +
960S GLU* 2.5 45.0 + - - +
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Residues in contact with GLU 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ALA* 3.0 20.1 + - + +
10L LYS* 3.7 4.3 - - - +
11L ASP 3.1 0.6 - - - -
12L ARG* 1.3 81.2 - - + +
14L ALA* 1.3 63.0 + - - +
16L GLU* 3.1 29.0 + - - +
17L GLY 3.3 5.4 + - - -
18L LEU* 3.2 36.1 + - + +
23L ARG* 3.6 11.8 + - - +
948S LYS* 3.5 34.7 - - - +
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Residues in contact with ALA 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L LYS* 2.7 40.8 + - + +
11L ASP* 3.9 6.3 - - - +
13L GLU* 1.3 71.4 - - - +
15L ALA* 1.3 62.1 + - - +
16L GLU 3.4 0.2 + - - -
17L GLY 4.0 6.3 + - - +
18L LEU* 3.6 23.5 - - - +
148L GLU* 5.0 5.6 - - - +
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Residues in contact with ALA 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ASP 2.8 18.9 + - - +
12L ARG* 3.5 10.1 - - - +
14L ALA* 1.3 78.6 - - - +
16L GLU* 1.3 60.9 + - + +
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Residues in contact with GLU 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ARG 3.2 13.2 + - - +
13L GLU* 3.1 21.6 + - - +
14L ALA 4.4 0.2 - - - -
15L ALA* 1.3 81.1 - - + +
17L GLY* 1.3 58.8 + - - +
23L ARG* 3.2 17.7 + - - +
948S LYS* 5.1 7.6 - - - -
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Residues in contact with GLY 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L GLU 3.3 1.0 + - - -
14L ALA 4.0 4.8 + - - +
15L ALA 3.8 0.4 - - - -
16L GLU* 1.3 77.9 - - - +
18L LEU* 1.3 71.0 + - - +
19L GLY 3.8 0.2 - - - -
20L SER* 3.2 23.8 + - - -
23L ARG* 2.6 27.6 - - - +
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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