Contacts of the helix formed by residues 41 - 54 (chain A) in PDB entry 1KB6
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 CYS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A CYS* 3.5 9.6 - - + +
27A CYS* 3.7 0.2 - - - -
29A ASP* 4.0 9.0 - - + +
30A ARG 3.6 23.1 - - - +
31A ALA* 4.2 0.4 - - - +
32A THR* 4.3 2.7 - - - +
35A HIS* 4.8 0.6 - - - -
40A THR* 1.3 80.6 + - - +
42A GLU* 1.3 65.7 + - - +
43A GLY 3.2 5.4 - - - -
44A CYS* 3.2 23.7 + - - -
45A LYS* 3.2 18.4 + - - +
73A ARG* 3.2 23.8 - - - -
150A ZN 2.4 34.1 - - - -
430D A 6.0 0.7 - - - +
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Residues in contact with GLU 42 (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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30A ARG 5.0 0.2 + - - -
32A THR* 2.6 42.9 + - + +
35A HIS* 3.7 6.1 + - - -
41A CYS* 1.3 73.6 - - - +
43A GLY* 1.3 62.8 + - - +
45A LYS* 2.8 34.4 + - - +
46A GLY* 3.1 20.1 + - - -
429D C 4.4 3.6 - - - +
430D A 3.6 37.4 + - + +
431D C 2.6 37.5 + - + +
432D C 5.2 1.1 + - - -
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Residues in contact with GLY 43 (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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41A CYS* 3.2 8.6 - - - -
42A GLU* 1.3 80.6 - - - +
44A CYS* 1.3 57.4 + - - +
47A PHE* 2.8 25.1 + - - +
73A ARG* 4.9 2.4 - - - +
80A ARG* 3.1 15.3 + - - -
429D C 3.6 38.7 + - - +
430D A 4.6 1.4 + - - -
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Residues in contact with CYS 44 (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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24A CYS* 4.1 6.7 - - - -
26A VAL* 3.7 26.5 - - + -
27A CYS* 3.8 4.9 - - - -
40A THR* 4.3 6.5 - - + -
41A CYS* 3.2 10.1 + - - +
43A GLY* 1.3 75.5 - - - +
45A LYS* 1.3 66.3 + - - +
47A PHE* 3.9 2.2 - - - +
48A PHE* 2.9 27.0 + - - +
80A ARG* 3.1 30.7 - - - +
84A CYS* 4.5 4.0 - - - -
89A MET* 4.0 3.9 - - - +
150A ZN 2.3 35.9 - - - -
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Residues in contact with LYS 45 (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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35A HIS* 3.3 47.3 - - + +
36A PHE* 3.8 17.5 - - + -
40A THR* 4.2 1.0 + - - +
41A CYS 3.2 12.1 + - - +
42A GLU* 2.8 39.8 + - - +
44A CYS* 1.3 76.6 - - - +
46A GLY* 1.3 69.1 + - - +
48A PHE* 3.6 1.2 - - - +
49A ARG* 2.9 36.3 + - - +
89A MET* 4.4 7.2 - - - -
403C C 6.2 0.2 - - - -
404C G 4.6 6.6 + - - -
405C G 2.9 40.1 + - - -
406C G 4.6 5.4 - - - -
431D C 4.1 0.4 - - - +
432D C 4.2 3.0 - - - +
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Residues in contact with GLY 46 (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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42A GLU 3.1 9.1 + - - -
43A GLY 3.9 1.8 - - - -
45A LYS* 1.3 86.0 - - - +
47A PHE* 1.3 63.8 + - - +
49A ARG* 4.1 12.0 - - - +
50A ARG* 3.2 25.5 + - - +
429D C 5.0 15.7 - - - -
430D A 5.9 1.3 - - - -
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Residues in contact with PHE 47 (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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43A GLY 2.8 22.1 + - - +
44A CYS 3.9 1.8 - - - +
46A GLY* 1.3 72.9 - - - +
48A PHE* 1.3 60.8 + - - +
50A ARG* 4.0 1.3 - - - +
51A SER* 2.6 53.2 + - - -
58A PHE* 3.7 12.8 - + - -
77A GLN* 3.6 33.7 - - + -
80A ARG* 3.7 37.7 - - + +
81A LEU* 3.6 32.1 - - + -
84A CYS* 4.4 6.7 - - - -
428D T 3.5 40.9 + - - +
429D C 4.9 1.7 - - - +
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Residues in contact with PHE 48 (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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36A PHE* 3.5 42.0 - + + -
44A CYS 2.9 21.0 + - - +
45A LYS 3.7 1.1 - - - +
47A PHE* 1.3 81.8 - - - +
49A ARG* 1.3 65.4 + - - +
51A SER* 3.9 3.3 - - - -
52A MET* 3.1 51.4 + - + +
81A LEU* 3.8 9.6 - - + -
84A CYS* 3.6 25.6 - - + -
85A VAL* 4.3 7.2 - - + -
89A MET* 3.8 29.2 - - + -
90A MET 3.9 3.1 - - - -
91A LYS 3.7 20.6 - - - -
94A ILE* 4.0 12.8 - - + -
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Residues in contact with ARG 49 (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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36A PHE* 3.8 19.1 - - + -
45A LYS* 2.9 34.9 + - - +
46A GLY* 4.1 10.3 - - - +
48A PHE* 1.3 72.1 - - - +
50A ARG* 1.3 63.4 + - - +
52A MET* 3.1 4.0 + - - +
53A LYS* 2.8 46.0 + - + +
94A ILE* 3.9 24.6 - - + +
405C G 3.0 61.1 + - - +
406C G 3.4 33.7 + - - -
407C T 5.2 5.1 + - - +
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Residues in contact with ARG 50 (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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46A GLY 3.2 16.3 + - - +
47A PHE* 4.0 2.5 - - - +
49A ARG* 1.3 79.5 - - - +
51A SER* 1.3 64.4 + - - +
53A LYS* 4.5 6.1 - - - -
54A ARG* 3.1 69.6 + - - +
426D A 3.9 6.7 - - - +
427D T 2.2 62.6 + - - +
428D T 4.0 39.3 + - - +
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Residues in contact with SER 51 (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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47A PHE* 2.6 43.8 + - - -
48A PHE 3.9 3.6 - - - -
50A ARG* 1.3 80.8 - - - +
52A MET* 1.3 63.0 + - - +
55A LYS* 3.4 1.2 + - - -
56A ALA* 3.0 34.4 + - - +
58A PHE* 3.6 21.4 - - - -
81A LEU* 4.1 19.0 - - - +
428D T 5.0 1.7 + - - -
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Residues in contact with MET 52 (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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48A PHE* 3.1 49.0 + - + +
49A ARG 3.1 1.4 + - - -
51A SER* 1.3 75.2 - - - +
53A LYS* 1.3 70.7 + - - +
55A LYS* 3.2 15.9 + - - +
81A LEU* 4.5 15.3 - - + -
85A VAL* 4.1 17.9 - - + -
91A LYS* 4.0 32.3 - - + +
94A ILE* 3.6 17.7 - - + -
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Residues in contact with LYS 53 (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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49A ARG* 2.8 42.2 + - + +
50A ARG* 3.9 4.3 - - - +
52A MET* 1.3 75.7 - - - +
54A ARG* 1.3 65.0 - - - +
55A LYS* 2.2 31.9 + - - +
94A ILE* 4.2 13.9 - - + +
95A LEU 4.6 12.6 + - - -
96A THR* 5.9 0.7 - - - +
97A ASP* 3.9 22.8 + - - -
100A VAL* 5.3 6.3 - - - +
405C G 5.5 2.4 + - - -
406C G 3.8 20.6 + - - -
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Residues in contact with ARG 54 (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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50A ARG* 3.1 68.6 + - - +
51A SER 4.7 0.7 - - - +
53A LYS* 1.3 81.6 - - - +
55A LYS* 1.3 71.1 + - - +
56A ALA* 2.9 9.6 + - + +
427D T 4.3 7.6 + - - -
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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