Contacts of the helix formed by residues 32 - 43 (chain A) in PDB entry 2HEI
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ALA 3.3 0.4 - - - -
31A VAL* 1.3 80.9 - - - +
33A LYS* 1.3 61.6 + - - +
34A SER 3.3 2.2 - - - -
35A SER* 3.7 0.9 - - - -
36A LEU* 2.8 37.8 + - - +
133A ASN* 3.6 10.1 - - - -
201A GDP 3.1 31.1 + - - -
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Residues in contact with LYS 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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25A LEU* 3.6 20.7 - - + +
26A LEU 3.5 34.5 - - - +
27A GLY 2.9 16.6 + - - -
28A GLU 3.1 8.9 + - - -
31A VAL* 3.9 9.1 - - + +
32A GLY* 1.3 76.9 - - - +
34A SER* 1.3 64.2 + - - +
36A LEU 3.3 0.2 + - - -
37A VAL* 3.1 27.2 + - - +
75A ASP* 3.5 12.3 - - - +
76A THR* 3.7 11.7 - - - +
77A ALA* 3.7 19.5 - - - +
80A GLU* 2.8 29.3 + - - -
99A VAL* 4.0 9.0 - - + -
201A GDP 2.6 27.2 + - - +
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Residues in contact with SER 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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33A LYS* 1.3 75.3 - - - +
35A SER* 1.3 58.0 - - - +
37A VAL* 3.2 3.6 + - - +
38A LEU* 2.9 36.0 + - - +
50A GLU 5.1 0.9 - - - -
51A SER* 4.1 1.1 - - - -
52A THR 3.2 31.1 + - - -
53A ILE* 3.8 3.3 - - - +
75A ASP* 2.7 25.7 + - - -
77A ALA* 3.2 8.8 - - - +
201A GDP 2.7 27.3 + - - -
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Residues in contact with SER 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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32A GLY 3.7 1.8 - - - -
34A SER* 1.3 75.5 - - - +
36A LEU* 1.3 56.3 + - - +
38A LEU* 3.5 7.4 + - - +
39A ARG* 2.9 30.1 + - - +
44A GLN 4.8 0.9 - - - +
45A PHE* 4.0 12.5 - - - -
46A HIS 5.6 0.5 + - - -
164A ALA* 3.6 13.9 - - - +
201A GDP 2.6 62.6 + - - -
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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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25A LEU* 4.4 8.7 - - + -
32A GLY 2.8 20.5 + - - +
33A LYS 3.7 4.0 - - - +
34A SER 3.2 0.2 - - - -
35A SER* 1.3 77.3 - - - +
37A VAL* 1.3 63.0 + - - +
39A ARG* 3.4 3.4 + - - +
40A PHE* 3.0 23.9 + - - +
97A ILE* 5.6 1.6 - - + -
99A VAL* 3.8 37.0 - - + -
131A ALA* 4.6 6.5 - - + -
133A ASN* 3.6 18.2 - - - +
162A THR* 3.6 24.9 - - + +
164A ALA* 4.1 6.3 - - + +
170A VAL* 3.6 34.1 - - + +
173A LEU* 6.2 1.3 - - + -
174A PHE* 4.6 7.1 - - + -
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Residues in contact with VAL 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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25A LEU* 3.6 33.2 - - + -
33A LYS 3.1 16.3 + - - +
34A SER 3.7 0.2 - - - +
36A LEU* 1.3 75.7 - - - +
38A LEU* 1.3 57.5 + - - +
40A PHE* 3.1 5.5 + - - +
41A VAL* 2.8 44.6 + - + +
53A ILE* 3.7 27.6 - - + -
58A LEU* 4.3 9.6 - - + -
73A ILE* 3.7 24.0 - - + -
75A ASP* 4.9 6.7 - - + -
174A PHE* 5.1 3.4 - - + -
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Residues in contact with LEU 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 SER* 2.9 22.1 + - - +
35A SER* 4.0 5.8 - - - +
37A VAL* 1.3 74.7 - - - +
39A ARG* 1.3 57.9 + - - +
41A VAL* 4.9 0.2 - - - -
42A LYS* 2.8 47.8 + - + +
43A GLY 3.3 4.3 + - - -
44A GLN 3.8 8.1 - - - +
45A PHE* 6.2 0.4 - - - -
49A GLN* 4.0 20.6 - - + +
50A GLU 5.8 0.4 - - - +
52A THR 3.9 19.3 - - - +
53A ILE* 4.1 17.3 - - + +
58A LEU* 3.8 25.1 - - + -
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Residues in contact with ARG 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 SER 2.9 19.4 + - - +
36A LEU* 3.7 5.2 - - - +
38A LEU* 1.3 77.7 - - - +
40A PHE* 1.3 59.3 + - - +
43A GLY* 2.8 58.2 + - - -
44A GLN* 3.4 15.0 + - - +
45A PHE* 3.4 15.6 - - + +
164A ALA* 2.9 22.8 + - - +
165A LYS 2.9 29.7 + - - -
166A THR 3.7 6.5 + - - -
167A ALA* 3.5 29.7 - - + +
170A VAL* 4.0 19.5 - - + -
171A ASN* 4.6 4.7 - - - +
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Residues in contact with PHE 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 18.6 + - - +
37A VAL 3.7 2.7 - - - +
39A ARG* 1.3 78.3 - - - +
41A VAL* 1.3 63.1 + - - +
43A GLY* 4.4 1.4 + - - -
60A GLN* 3.3 46.2 + - + -
61A SER 4.0 2.7 - - - -
62A VAL* 3.7 22.4 - - + -
71A PHE* 4.1 9.6 - + - -
73A ILE* 3.7 24.7 - - + -
170A VAL* 4.1 3.8 - - + +
171A ASN* 3.4 31.7 - - - +
174A PHE* 3.6 58.1 - + + -
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Residues in contact with VAL 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 VAL* 2.8 29.9 + - + +
38A LEU 4.5 0.2 - - - +
40A PHE* 1.3 74.8 - - + +
42A LYS* 1.3 76.1 + - + +
58A LEU* 3.9 39.7 - - + -
59A THR 3.5 18.2 - - - +
60A GLN* 3.2 35.6 + - + -
73A ILE* 4.0 13.2 - - + -
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Residues in contact with LYS 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 LEU* 2.8 33.9 + - + +
41A VAL* 1.3 92.7 - - + +
43A GLY* 1.3 58.5 + - - +
44A GLN* 3.3 20.8 + - + +
58A LEU* 4.6 18.9 - - - +
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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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38A LEU 3.3 0.4 + - - -
39A ARG* 2.8 48.7 + - - -
40A PHE 4.4 1.7 + - - -
41A VAL 3.6 1.4 - - - -
42A LYS* 1.3 77.4 - - - +
44A GLN* 1.3 56.5 + - - +
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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