Contacts of the helix formed by residues 33 - 44 (chain H) in PDB entry 4KYI
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 GLY 33 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31H ALA 3.5 0.6 - - - -
32H VAL* 1.3 80.7 - - - +
34H LYS* 1.3 65.8 + - - +
35H SER 3.4 1.8 - - - -
36H SER* 3.8 1.7 - - - -
37H LEU* 3.2 32.5 + - - +
100H VAL* 4.8 1.3 - - - -
134H ASN* 3.5 8.1 + - - -
301H GNP 3.1 33.6 + - - -
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Residues in contact with LYS 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H LEU* 3.8 27.8 - - + +
27H LEU 3.8 4.9 - - - -
28H GLY* 3.7 29.4 + - - +
29H GLU 3.2 17.6 + - - -
32H VAL* 3.9 10.1 - - + -
33H GLY* 1.3 77.5 - - - +
35H SER* 1.3 62.9 + - - +
37H LEU* 3.7 2.8 + - - +
38H VAL* 3.2 27.4 + - - +
76H ASP* 3.4 12.1 - - - +
77H THR* 3.2 25.8 - - - +
79H GLY 4.1 4.2 - - - +
100H VAL* 4.1 14.4 - - + -
301H GNP 2.4 48.4 + - - +
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Residues in contact with SER 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H LYS* 1.3 76.6 - - - +
36H SER* 1.3 58.8 + - - +
37H LEU 3.4 0.2 - - - -
38H VAL* 3.6 3.7 + - - +
39H LEU* 3.0 29.3 + - - +
50H GLN* 4.3 18.2 + - - +
51H GLU 5.5 1.5 + - - -
53H THR* 2.9 5.2 + - - +
76H ASP* 2.5 22.1 + - - -
301H GNP 3.3 11.7 + - - -
302H MG 2.1 30.2 - - - -
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Residues in contact with SER 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLY 4.0 2.2 - - - -
34H LYS 3.3 0.4 - - - -
35H SER* 1.3 76.7 - - - +
37H LEU* 1.3 58.4 + - - +
39H LEU* 3.8 2.8 - - - +
40H ARG* 3.0 29.1 + - - +
45H GLN 4.3 2.6 - - - +
46H PHE* 4.1 10.2 - - - +
47H HIS 4.7 0.9 + - - -
50H GLN* 3.7 18.6 + - - -
165H ALA* 3.5 14.3 - - - +
301H GNP 3.1 53.0 + - - -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H LEU* 4.7 10.8 - - + -
33H GLY 3.2 22.7 + - - +
34H LYS 3.9 4.0 - - - +
36H SER* 1.3 74.1 - - - +
38H VAL* 1.3 54.3 + - - +
40H ARG* 3.2 4.4 + - - +
41H PHE* 2.8 37.3 + - - +
98H ILE* 5.4 2.7 - - + -
100H VAL* 4.1 30.3 - - + -
132H ALA* 4.9 5.4 - - + -
134H ASN* 3.4 20.4 - - - +
163H THR* 3.6 19.3 - - + +
165H ALA* 3.7 8.9 - - + +
171H VAL* 3.8 31.1 - - + +
174H ILE* 6.2 3.6 - - + -
175H PHE* 4.7 8.5 - - + -
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Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H LEU* 3.8 28.9 - - + -
34H LYS 3.2 17.4 + - - +
35H SER* 3.8 8.3 - - - +
36H SER 3.4 0.2 - - - -
37H LEU* 1.3 76.1 - - - +
39H LEU* 1.3 53.0 + - - +
41H PHE* 3.2 5.6 + - - -
42H VAL* 2.7 47.6 + - + +
59H LEU* 3.6 42.0 - - + -
74H ILE* 4.3 13.2 - - + -
76H ASP* 4.7 7.0 - - + +
175H PHE* 4.9 6.5 - - + -
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H SER 3.0 19.6 + - - +
36H SER* 3.8 4.9 - - - +
38H VAL* 1.3 75.6 - - - +
40H ARG* 1.3 57.3 + - - +
42H VAL* 4.8 1.8 - - + -
43H LYS* 2.9 41.2 + - + +
44H GLY 3.2 5.5 + - - -
45H GLN* 3.3 38.2 + - + +
46H PHE* 4.6 1.6 - - - +
47H HIS* 3.6 26.9 - - + +
50H GLN* 3.2 29.4 - - - +
59H LEU* 5.8 3.1 - - + -
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Residues in contact with ARG 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H SER 3.0 19.0 + - - +
37H LEU* 3.4 4.9 - - - +
39H LEU* 1.3 75.2 - - - +
41H PHE* 1.3 63.6 + - - +
44H GLY* 2.9 47.1 + - - -
45H GLN* 3.4 15.7 + - - +
46H PHE* 3.5 12.3 - - - +
165H ALA* 2.8 23.6 + - + +
166H LYS 2.7 30.1 + - - -
167H THR* 4.4 0.8 - - - +
168H ALA* 3.6 31.1 - - + +
171H VAL* 3.7 21.3 - - + -
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Residues in contact with PHE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LEU 2.8 20.4 + - - +
38H VAL* 3.8 3.1 - - - +
40H ARG* 1.3 76.4 - - - +
42H VAL* 1.3 69.4 + - + +
61H GLN* 3.6 36.9 + - + -
63H VAL* 3.8 28.5 - - + -
72H PHE* 4.4 10.1 - + - -
74H ILE* 4.1 16.6 - - + -
171H VAL* 4.4 4.9 - - + -
172H ASN* 3.8 31.9 - - - +
175H PHE* 3.5 56.5 - + + -
176H MET* 5.4 1.1 - - - -
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Residues in contact with VAL 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H VAL* 2.7 39.2 + - + +
39H LEU* 4.5 1.1 - - - +
41H PHE* 1.3 88.9 - - + +
43H LYS* 1.3 78.8 + - + +
44H GLY 3.7 0.2 - - - -
59H LEU* 3.9 24.5 - - + -
60H THR 5.2 3.6 - - - +
61H GLN* 3.8 34.6 + - + +
74H ILE* 4.8 2.0 - - + -
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Residues in contact with LYS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU* 2.9 28.0 + - + +
42H VAL* 1.3 95.1 - - + +
44H GLY* 1.3 65.4 + - - +
45H GLN* 3.4 32.5 + - - +
59H LEU* 5.8 4.9 - - - -
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Residues in contact with GLY 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU 3.2 0.4 + - - -
40H ARG* 2.9 42.1 + - - -
42H VAL 3.7 0.4 - - - -
43H LYS* 1.3 78.6 - - - +
45H GLN* 1.3 60.8 + - - +
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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