Contacts of the helix formed by residues 38 - 46 (chain E) in PDB entry 1GUM
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 LYS 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E THR* 1.3 74.8 - - + +
39E GLU* 1.3 51.8 + - - +
41E LEU* 2.8 9.6 - - + +
42E TYR* 2.6 70.5 + - + +
218E ASN 4.2 12.2 + - - +
219E ILE* 3.5 28.2 - - - +
220E PHE* 3.5 25.7 + - - +
182G GLN* 5.7 3.0 + - - +
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Residues in contact with GLU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E THR* 3.0 13.9 - - + +
38E LYS* 1.3 78.1 - - - +
40E GLN* 1.3 73.5 + - - +
42E TYR* 2.7 31.9 + - + +
43E LYS* 2.8 42.3 + - + +
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Residues in contact with GLN 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E GLU* 5.8 2.4 + - - -
34E PHE 3.6 14.9 + - - -
35E LEU* 4.0 13.5 - - + +
36E GLU* 2.5 45.7 + - - +
37E THR* 2.9 28.4 + - - +
39E GLU* 1.3 81.4 + - - +
41E LEU* 1.3 62.2 + - - +
43E LYS* 3.3 18.1 + - + +
44E LEU* 3.2 21.8 + - - +
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 3.9 22.1 - - + +
37E THR 3.0 10.5 + - - +
38E LYS* 2.8 15.5 - - + +
40E GLN* 1.3 75.9 - - - +
42E TYR* 1.3 63.4 + - + -
44E LEU* 2.8 16.8 + - + +
45E GLN* 2.9 35.1 + - - +
50E LEU* 3.9 22.4 - - + -
53E GLN 4.9 2.7 - - - +
54E GLN* 5.7 1.3 - - - -
55E VAL* 5.2 3.8 - - + -
219E ILE* 3.6 19.5 - - + +
220E PHE* 3.3 37.0 - - + -
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Residues in contact with TYR 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LYS* 2.6 54.5 + - + +
39E GLU* 2.7 23.6 + - + +
41E LEU* 1.3 71.5 - - + +
43E LYS* 1.3 52.2 + - + +
45E GLN* 3.0 24.3 + - + +
46E ASP* 2.4 41.8 + - + +
176G SER 3.7 19.9 + - - -
177G ALA* 6.1 1.3 - - - -
179G PRO* 4.1 32.2 - - + +
182G GLN* 4.3 11.6 + - - -
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Residues in contact with LYS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E GLU* 2.8 41.3 + - + +
40E GLN* 3.6 18.6 - - + +
41E LEU 3.1 0.4 - - - -
42E TYR* 1.3 77.9 - - + +
44E LEU* 1.3 58.8 + - - +
46E ASP* 3.9 9.3 - - - +
47E GLY* 2.7 26.3 + - - -
49E HIS* 3.8 3.1 + - - -
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E HIS* 4.0 37.2 - - + +
33E GLU* 5.1 5.2 - - - +
35E LEU* 3.9 28.9 - - + -
40E GLN 3.2 8.6 + - - +
41E LEU* 2.9 14.1 - - + +
43E LYS* 1.3 81.2 - - - +
45E GLN* 1.3 60.0 + - - +
47E GLY 3.3 0.2 + - - -
49E HIS* 2.9 60.1 + - + +
50E LEU* 3.9 23.1 - - + -
55E VAL* 4.7 0.9 - - + -
57E MET* 4.9 2.5 - - + -
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Residues in contact with GLN 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 2.9 38.3 + - + +
42E TYR* 3.1 40.6 - - + +
44E LEU* 1.3 78.7 - - - +
46E ASP* 1.3 51.9 + - - +
48E ASN* 2.7 32.9 + - - +
49E HIS 4.8 0.2 - - - +
50E LEU* 3.9 12.4 + - + +
53E GLN* 3.1 56.5 + - - +
131F ARG* 5.5 2.0 - - - +
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Residues in contact with ASP 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E TYR* 2.4 29.4 + - + +
43E LYS* 3.8 9.2 - - - +
45E GLN* 1.3 74.0 - - - +
47E GLY* 1.3 63.2 + - - +
48E ASN* 3.0 9.1 + - - +
141G ARG* 3.8 32.6 + - - -
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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