Contacts of the helix formed by residues 30 - 42 (chain A) in PDB entry 1KYZ
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A SER* 4.3 1.9 + - - -
29A ALA* 1.3 77.2 - - - +
31A VAL* 1.3 69.0 + - - +
32A LEU 3.3 0.6 + - - -
33A PRO* 3.3 6.5 - - - +
34A MET* 3.1 30.7 + - - +
30E SER* 5.5 2.2 - - - +
33E PRO* 3.8 12.2 - - - +
34E MET* 5.4 0.2 - - - -
131E ASN* 4.3 3.3 + - - +
132E GLN* 2.9 24.4 + - - -
137E MET* 3.6 36.4 - - - -
140E TRP* 4.1 7.2 + - - -
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Residues in contact with VAL 31 (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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28A SER* 3.3 18.6 - - - +
29A ALA 3.1 0.8 - - - -
30A SER* 1.3 80.6 + - - +
32A LEU* 1.3 57.6 + - - +
34A MET* 4.8 0.2 - - - -
35A ILE* 2.9 29.8 + - - +
83A LEU* 3.6 27.8 - - + -
140E TRP* 4.0 16.6 - - + -
315E HIS* 4.2 11.9 - - + +
318E VAL* 3.8 23.8 - - + -
319E ILE* 3.7 33.7 - - + -
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Residues in contact with LEU 32 (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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29A ALA* 3.6 6.3 + - - +
30A SER 3.3 0.2 - - - -
31A VAL* 1.3 79.1 - - - +
33A PRO* 1.3 68.0 - - + +
35A ILE* 4.0 0.9 - - - +
36A LEU* 2.9 32.3 + - + +
83A LEU* 4.0 8.5 - - + +
84A LEU* 4.4 7.5 - - + +
87A TYR* 3.9 48.5 - - + +
89A ILE* 3.7 29.6 - - + -
9E ILE* 4.8 6.7 - - + -
10E THR* 4.0 13.5 - - + -
26E LEU* 3.5 25.8 - - + -
29E ALA* 4.6 6.7 - - + -
315E HIS* 5.4 2.0 + - + +
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Residues in contact with PRO 33 (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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29A ALA 3.2 13.2 - - - +
30A SER* 3.3 14.4 - - - +
32A LEU* 1.3 102.5 - - + +
34A MET* 1.3 57.4 + - + +
36A LEU* 3.8 5.8 - - + +
37A LYS* 2.9 29.1 + - - +
128A ASN* 5.7 0.5 - - - +
132A GLN* 4.1 18.3 - - + +
26E LEU* 4.4 7.0 - - + +
29E ALA* 3.8 14.8 - - + -
30E SER* 3.7 38.4 - - - +
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Residues in contact with MET 34 (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 SER* 3.1 26.2 + - - +
31A VAL 4.2 0.9 - - - +
33A PRO* 1.3 75.7 - - + +
35A ILE* 1.3 61.8 + - - +
37A LYS* 3.3 9.7 + - + +
38A SER* 3.0 32.0 + - - -
132A GLN* 3.7 33.2 - - + +
137A MET* 4.1 14.8 - - + -
30E SER* 5.0 0.4 - - - -
137E MET* 4.4 2.0 - - + -
140E TRP* 3.6 51.3 - - + +
141E TYR* 3.6 37.0 - - + +
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Residues in contact with ILE 35 (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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31A VAL* 2.9 24.8 + - + +
34A MET* 1.3 71.9 - - - +
36A LEU* 1.3 62.7 + - - +
38A SER* 3.2 4.8 + - - -
39A ALA* 2.9 26.7 + - - +
80A MET* 3.8 37.4 - - + +
83A LEU* 3.7 18.8 - - + -
84A LEU* 4.0 10.8 - - + -
140E TRP* 3.9 6.3 - - + -
143E LEU* 3.5 29.2 - - + -
318E VAL* 3.3 36.3 - - + -
321E LEU* 5.5 0.2 - - + -
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Residues in contact with LEU 36 (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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32A LEU* 2.9 18.8 + - + +
33A PRO* 3.8 5.8 - - + +
35A ILE* 1.3 78.9 - - - +
37A LYS* 1.3 62.2 + - - +
39A ALA* 3.1 8.7 + - + +
40A LEU* 3.0 43.2 + - + +
45A LEU* 4.8 4.3 - - + -
84A LEU* 4.0 22.6 - - + +
89A ILE* 4.4 15.5 - - + -
115A LEU* 4.6 13.5 - - + -
128A ASN* 3.4 24.9 - - - +
26E LEU* 3.8 37.7 - - + +
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Residues in contact with LYS 37 (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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33A PRO 2.9 19.0 + - - +
34A MET* 3.5 14.6 - - + +
35A ILE 3.2 0.2 - - - -
36A LEU* 1.3 76.4 - - - +
38A SER* 1.3 58.9 + - - +
40A LEU* 3.1 12.9 + - - +
41A GLU* 2.9 55.3 + - - +
128A ASN* 4.0 15.0 - - + +
129A LEU* 4.0 26.5 - - + +
132A GLN* 3.0 39.3 + - + +
133A ASP* 3.7 13.4 + - - +
134A LYS 4.3 0.6 - - - +
140E TRP 6.1 0.9 - - - +
141E TYR* 3.7 21.0 - - + +
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Residues in contact with SER 38 (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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34A MET 3.0 17.7 + - - -
35A ILE 3.2 4.5 + - - -
37A LYS* 1.3 78.5 - - - +
39A ALA* 1.3 62.4 + - - +
41A GLU* 3.2 17.4 + - - +
42A LEU* 3.0 28.7 + - - +
80A MET* 3.8 17.9 - - - -
140E TRP* 3.6 20.6 + - - -
143E LEU* 3.7 18.8 - - - +
144E LYS* 4.8 4.0 - - - +
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Residues in contact with ALA 39 (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 ILE 2.9 13.6 + - - +
36A LEU* 3.1 12.5 + - + +
38A SER* 1.3 75.1 - - - +
40A LEU* 1.3 62.4 + - + +
42A LEU 3.2 1.4 + - - -
43A ASP 3.1 3.6 + - - -
44A LEU* 3.0 57.1 + - + +
45A LEU* 4.6 5.6 + - + -
80A MET* 4.1 4.9 - - + +
84A LEU* 3.9 23.1 - - + -
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Residues in contact with LEU 40 (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 LEU* 3.0 26.7 + - + +
37A LYS* 3.1 7.4 + - - +
39A ALA* 1.3 74.0 - - - +
41A GLU* 1.3 63.3 + - - +
42A LEU 3.1 1.6 - - - -
43A ASP* 3.2 18.5 + - - +
44A LEU 5.1 0.2 - - - +
45A LEU* 3.6 35.4 - - + -
115A LEU* 4.9 5.4 - - + +
125A SER* 3.8 27.6 - - - +
128A ASN* 3.4 42.2 - - + +
129A LEU* 4.2 16.9 - - + +
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Residues in contact with GLU 41 (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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37A LYS* 2.9 43.5 + - - +
38A SER* 3.6 23.5 + - - +
40A LEU* 1.3 76.9 - - - +
42A LEU* 1.3 60.0 + - - +
43A ASP* 3.7 4.7 + - - +
129A LEU* 3.6 18.3 - - + +
140E TRP 4.9 4.0 - - - +
141E TYR* 5.1 7.4 - - - +
144E LYS* 3.7 39.9 + - + +
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Residues in contact with LEU 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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38A SER 3.0 19.0 + - - +
39A ALA 3.2 4.0 + - - +
40A LEU 3.1 0.2 - - - -
41A GLU* 1.3 77.6 - - - +
43A ASP* 1.3 68.9 + - - +
44A LEU* 3.2 12.8 + - + -
47A ILE* 4.1 0.3 - - - +
66A LEU* 3.5 23.1 - - + +
77A LEU* 4.2 13.0 - - + -
80A MET* 4.2 16.8 - - + -
144E LYS* 3.4 33.2 - - + +
147E VAL* 4.1 28.0 - - + -
148E LEU* 3.8 31.2 - - + -
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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