Contacts of the helix formed by residues 38 - 53 (chain A) in PDB entry 4KPD
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 ILE 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A HIS* 3.4 31.6 - - + +
37A GLU* 1.3 87.3 - - + +
39A GLY* 1.3 57.7 + - - +
40A ASP 3.4 2.5 - - - -
41A ALA* 3.1 16.0 + - + +
42A ILE* 2.9 54.6 + - + +
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Residues in contact with GLY 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 HIS 4.4 2.0 + - - -
36A PRO* 3.2 18.3 + - - -
37A GLU 3.3 1.4 - - - -
38A ILE* 1.3 76.5 - - - +
40A ASP* 1.4 58.6 + - - +
42A ILE* 3.4 6.5 + - - +
43A ALA* 2.9 29.2 + - - +
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Residues in contact with ASP 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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37A GLU 5.0 2.5 + - - +
38A ILE 3.4 0.6 - - - -
39A GLY* 1.4 74.0 - - - +
41A ALA* 1.4 58.3 + - - +
43A ALA* 3.4 8.5 + - - +
44A ARG* 3.0 27.5 + - - +
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Residues in contact with ALA 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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38A ILE* 3.1 20.2 + - + +
40A ASP* 1.4 75.5 - - - +
42A ILE* 1.3 59.7 + - + +
44A ARG* 3.2 10.0 + - - +
45A LEU* 2.9 26.7 + - - +
134A LEU* 5.1 5.4 - - + +
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Residues in contact with ILE 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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28A LEU 4.2 14.1 - - - +
29A THR* 3.6 38.2 - - + +
30A GLU 5.0 4.9 - - - +
38A ILE* 2.9 47.0 + - + +
39A GLY* 3.8 5.8 - - - +
41A ALA* 1.3 72.9 - - + +
43A ALA* 1.3 64.4 + - - +
45A LEU* 3.2 16.7 + - + +
46A LYS* 3.1 22.2 + - - +
141A ARG* 4.8 7.0 - - - +
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Residues in contact with ALA 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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39A GLY 2.9 18.6 + - - +
40A ASP* 3.4 10.1 - - - +
41A ALA 3.3 0.2 - - - -
42A ILE* 1.3 77.4 - - - +
44A ARG* 1.4 60.7 + - - +
46A LYS* 3.4 10.7 + - - +
47A GLU* 3.2 19.6 + - - +
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Residues in contact with ARG 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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40A ASP 3.0 14.1 + - - +
41A ALA* 3.2 12.1 + - - +
43A ALA* 1.4 73.0 - - - +
45A LEU* 1.4 60.0 + - - +
47A GLU* 3.2 24.0 + - - +
48A VAL* 2.9 34.4 + - + +
118A TRP* 3.7 12.6 - - - -
123A GLY 4.4 11.1 + - - -
124A VAL* 3.9 17.4 - - - +
127A ASP* 3.8 24.4 + - - +
131A ASP* 2.9 42.0 + - - +
134A LEU* 5.6 4.3 - - + -
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Residues in contact with LEU 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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28A LEU* 3.9 21.5 - - + +
29A THR* 5.0 1.3 - - + -
41A ALA 2.9 13.8 + - - +
42A ILE* 3.2 21.1 + - + +
44A ARG* 1.4 73.9 - - - +
46A LYS* 1.3 59.7 + - - +
48A VAL* 3.3 11.5 + - + +
49A LEU* 2.9 49.9 + - + +
134A LEU* 4.1 37.7 - - + +
135A LEU 5.1 0.4 - - - +
138A CYS* 3.7 33.2 - - - -
141A ARG* 4.0 7.6 - - - +
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Residues in contact with LYS 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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25A VAL* 3.8 20.3 - - + +
29A THR* 3.8 25.2 + - + +
42A ILE 3.1 8.2 + - - +
43A ALA* 3.5 11.9 - - - +
44A ARG 3.3 0.2 - - - -
45A LEU* 1.3 75.0 - - - +
47A GLU* 1.4 56.9 + - - +
49A LEU* 3.2 7.7 + - - +
50A GLU* 2.9 58.9 + - - +
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Residues in contact with GLU 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 ALA 3.2 9.1 + - - +
44A ARG* 3.2 29.2 + - - +
46A LYS* 1.4 78.2 - - - +
48A VAL* 1.3 56.2 + - - +
50A GLU* 4.1 5.6 - - - +
51A TYR* 3.1 32.7 + - + +
118A TRP* 4.0 22.4 - - + -
121A LYS* 6.0 1.2 - - - +
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Residues in contact with VAL 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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44A ARG* 2.9 22.8 + - + +
45A LEU* 3.5 15.3 - - + +
47A GLU* 1.3 75.7 - - - +
49A LEU* 1.3 56.1 + - - +
52A ASN* 2.9 47.9 + - - +
101A VAL* 6.0 0.2 - - + -
118A TRP* 3.8 14.1 - - + -
131A ASP* 3.5 47.3 - - + +
134A LEU* 5.4 2.0 - - + -
135A LEU* 3.8 30.5 - - + -
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Residues in contact with LEU 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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21A PHE* 3.4 17.5 - - + -
24A ILE* 5.6 0.7 - - + -
25A VAL* 4.4 14.8 - - + -
28A LEU* 4.0 33.0 - - + -
29A THR* 4.6 4.5 - - + -
45A LEU* 2.9 43.5 + - + +
46A LYS* 3.5 9.0 - - - +
48A VAL* 1.3 72.1 - - - +
50A GLU* 1.3 57.7 + - - +
53A ALA* 3.0 33.1 + - - +
94A LEU* 3.7 30.1 - - + -
135A LEU* 3.8 14.1 - - + -
138A CYS* 4.6 7.4 - - - -
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Residues in contact with GLU 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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21A PHE* 4.2 13.5 - - + -
25A VAL* 3.6 32.2 - - - +
46A LYS* 2.9 48.1 + - - +
47A GLU* 4.1 4.7 - - - +
49A LEU* 1.3 74.9 - - - +
51A TYR* 1.3 61.1 + - - +
54A ILE* 3.6 22.6 - - + +
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Residues in contact with TYR 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 GLU 3.1 19.3 + - - +
50A GLU* 1.3 77.8 - - - +
52A ASN* 1.3 73.1 + - - +
54A ILE 3.9 7.8 - - - +
113A ARG* 5.4 0.5 + - - -
115A GLN* 3.0 58.2 + - + +
116A ILE* 2.5 44.1 + - - +
117A CYS* 5.1 0.2 - - - -
118A TRP* 3.5 43.7 - + + -
121A LYS* 3.7 27.7 + - + -
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Residues in contact with ASN 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 VAL* 2.9 34.1 + - - +
51A TYR* 1.3 86.0 - - - +
53A ALA* 1.3 58.5 + - - +
54A ILE 3.5 1.3 - - - -
97A ALA* 3.4 13.2 - - - +
101A VAL* 3.3 30.4 - - + +
113A ARG* 2.8 21.1 + - - +
118A TRP* 3.3 45.4 + - - +
135A LEU* 4.1 11.0 - - + -
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Residues in contact with ALA 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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21A PHE* 3.7 20.2 - - + -
49A LEU* 3.0 20.5 + - - +
52A ASN* 1.3 76.7 - - - +
54A ILE* 1.3 59.7 + - - +
58A TYR* 3.6 9.5 - - - -
90A TRP* 3.5 21.2 - - + -
93A GLU* 4.6 10.3 - - - +
94A LEU* 4.3 19.7 - - + -
97A ALA* 4.4 7.9 - - + -
113A ARG* 4.1 6.4 + - - +
135A LEU* 5.2 0.7 - - + -
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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