Contacts of the helix formed by residues 75 - 87 (chain D) in PDB entry 4KEU
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 ASP 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B GLN* 5.4 3.7 + - - +
26D ARG* 2.9 33.0 + - - +
28D PHE* 4.9 4.4 - - + -
42D GLU* 4.8 3.8 - - - +
73D GLY 3.3 5.5 + - - +
74D ARG* 1.3 77.6 - - - +
76D ILE* 1.3 63.1 + - - +
77D ARG* 3.2 21.5 + - - +
78D PHE* 3.1 13.8 + - + +
79D MET* 3.0 29.0 + - - +
127D GLN* 3.6 6.7 + - - +
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Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.7 30.1 - - + -
74D ARG* 4.6 2.3 - - + +
75D ASP* 1.3 72.9 - - - +
77D ARG* 1.3 67.7 + - - +
79D MET* 3.3 10.3 + - - +
80D GLU* 2.8 26.7 + - - +
92D ALA* 3.9 16.4 - - + -
126D ILE* 3.7 25.4 - - + +
127D GLN* 2.9 24.4 - - - +
129D THR* 3.6 30.1 - - + +
131D ASN* 3.6 30.7 - - + +
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Residues in contact with ARG 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ASP* 3.2 9.2 + - - +
76D ILE* 1.3 83.3 - - + +
78D PHE* 1.3 66.1 + - - +
80D GLU* 3.2 21.8 + - - +
81D LYS* 3.1 31.1 + - + +
127D GLN* 2.9 43.2 + - - +
128D GLY* 4.2 8.1 + - - -
129D THR* 3.5 17.9 - - + +
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Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.1 18.4 - - + -
26D ARG* 3.5 67.3 - - + +
42D GLU* 3.9 14.8 - - - +
45D GLU* 3.7 21.8 - - + -
46D PHE* 3.7 35.2 - + + -
49D ALA* 4.2 6.5 - - + -
75D ASP* 3.1 17.2 + - + +
77D ARG* 1.3 77.9 - - - +
79D MET* 1.3 68.8 + - + +
81D LYS* 3.3 14.1 + - + +
82D VAL* 3.1 29.3 + - + +
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Residues in contact with MET 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.9 7.6 - - + -
25D LEU* 4.2 13.5 - - + -
66D ASP* 3.3 41.1 - - + +
68D THR* 4.1 22.7 - - + +
74D ARG* 4.6 8.1 - - + -
75D ASP 3.0 18.9 + - - +
76D ILE* 3.3 17.9 - - - +
78D PHE* 1.3 81.4 - - + +
80D GLU* 1.4 62.1 + - - +
82D VAL* 3.1 4.2 + - - +
83D VAL* 3.0 26.2 + - - +
90D LEU* 3.7 20.0 - - + +
92D ALA* 3.9 25.1 - - + -
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.7 14.8 - - + +
7D GLY* 4.7 7.5 - - - +
76D ILE* 2.8 18.4 + - - +
77D ARG* 3.5 29.8 - - - +
79D MET* 1.4 70.5 - - - +
81D LYS* 1.3 65.4 + - + +
83D VAL* 3.1 5.9 + - - +
84D LYS* 3.0 44.7 + - - +
129D THR* 4.6 7.4 - - - +
131D ASN* 2.5 33.9 + - - +
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Residues in contact with LYS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLU* 5.0 14.0 + - - +
46D PHE* 3.6 29.6 - - + +
77D ARG* 3.1 17.4 + - + +
78D PHE* 3.5 14.3 - - + +
80D GLU* 1.3 78.6 - - + +
82D VAL* 1.3 61.0 + - - +
84D LYS* 3.4 12.6 + - - +
85D ALA* 3.1 24.6 + - - +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 3.9 21.5 - - + -
46D PHE* 4.0 18.8 - - + -
49D ALA* 4.1 14.6 - - + +
50D VAL* 4.5 4.5 - - + -
53D VAL* 4.2 21.1 - - + -
78D PHE* 3.1 34.2 + - + +
79D MET 3.1 9.2 + - - +
81D LYS* 1.3 73.4 - - - +
83D VAL* 1.3 60.2 + - + +
85D ALA* 3.4 2.8 + - - -
86D THR* 2.7 41.9 + - + +
88D ILE* 5.0 4.0 - - + -
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.4 31.2 - - + +
7D GLY* 4.7 6.3 - - - +
8D LYS* 4.4 16.6 - - + -
79D MET 3.0 17.5 + - - +
80D GLU* 3.1 8.7 + - - +
82D VAL* 1.3 77.7 - - - +
84D LYS* 1.3 62.1 + - + +
86D THR* 3.0 5.3 + - - -
87D GLY* 2.6 31.9 + - - -
88D ILE* 3.9 18.6 - - + +
90D LEU* 3.8 31.0 - - + -
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Residues in contact with LYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLY* 5.9 6.7 - - - +
80D GLU* 3.0 41.8 + - - +
81D LYS* 4.0 11.0 - - - +
83D VAL* 1.3 80.7 - - + +
85D ALA* 1.3 59.2 + - - +
86D THR 3.3 0.4 + - - -
87D GLY 4.7 0.7 + - - -
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PHE* 3.8 21.1 - - + -
50D VAL* 4.1 13.0 - - + +
54D LYS* 3.9 16.5 + - - -
81D LYS 3.1 16.8 + - - +
82D VAL 3.9 4.0 - - - +
83D VAL 3.1 0.6 - - - -
84D LYS* 1.3 77.7 - - - +
86D THR* 1.3 61.8 + - - +
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL* 3.7 35.4 - - + +
53D VAL* 3.7 22.2 - - + +
54D LYS* 4.4 9.0 - - - +
57D MET* 3.5 20.5 - - - +
82D VAL* 2.7 24.6 + - + +
83D VAL 3.0 0.4 + - - -
84D LYS 3.3 0.8 - - - -
85D ALA* 1.3 85.6 - - - +
87D GLY* 1.3 63.0 + - - +
88D ILE* 3.1 22.5 - - - +
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LYS* 2.5 32.3 + - - -
57D MET* 4.2 7.2 - - - +
83D VAL 2.6 21.8 + - - -
84D LYS 4.7 0.8 - - - -
86D THR* 1.3 72.1 - - - +
88D ILE* 1.3 58.0 + - - +
89D ASN* 3.7 0.5 + - - -
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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