Contacts of the helix formed by residues 8 - 18 (chain E) in PDB entry 1W88
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 PRO 8 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E GLN 3.5 6.9 - - - +
7E PHE* 1.3 84.0 - - + +
9E PHE* 1.3 60.3 + - - +
10E ALA 3.6 1.8 - - - -
11E GLU* 4.0 18.2 - - + +
12E GLN* 3.1 28.0 + - - +
19G GLN* 5.2 0.8 - - - +
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Residues in contact with PHE 9 (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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7E PHE* 2.5 45.2 + + + +
8E PRO* 1.3 71.0 - - - +
10E ALA* 1.3 61.7 + - - +
11E GLU 3.2 0.2 - - - -
12E GLN* 3.1 11.2 + - - +
13E LEU* 3.0 36.9 + - + +
229G PRO* 3.4 30.5 - - + +
230G GLY 5.0 1.6 - - - -
231G ILE* 3.5 37.9 - - + -
247G ALA* 5.1 8.3 - - + -
248G ALA 5.6 0.9 - - - -
251G ARG* 3.9 43.5 - - + +
259G THR* 4.1 9.4 - - + -
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Residues in contact with ALA 10 (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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9E PHE* 1.3 77.9 - - - +
11E GLU* 1.3 61.4 + - - +
13E LEU* 3.5 11.0 + - - +
14E GLU* 3.3 24.6 + - - +
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Residues in contact with GLU 11 (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 PRO* 3.9 22.5 + - + +
9E PHE 3.2 0.2 - - - -
10E ALA* 1.3 75.5 - - - +
12E GLN* 1.3 60.2 + - - +
14E GLU* 3.6 4.3 + - - +
15E LYS* 3.0 33.4 + - - +
19G GLN* 4.2 3.4 - - - +
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Residues in contact with GLN 12 (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 PRO 3.1 20.0 + - - +
9E PHE* 3.1 9.8 + - - +
11E GLU* 1.3 78.0 - - - +
13E LEU* 1.3 65.3 + - + +
15E LYS* 3.4 1.2 + - - +
16E VAL* 3.1 28.1 + - + +
19G GLN* 2.8 49.8 + - + +
20G PHE* 3.5 16.9 - - + -
224G VAL* 5.7 1.4 - - + +
228G ILE 4.6 1.0 - - - +
229G PRO* 3.6 11.2 - - - +
230G GLY 2.9 45.0 + - - -
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Residues in contact with LEU 13 (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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9E PHE* 3.0 25.7 + - + +
10E ALA* 4.1 8.5 - - - +
11E GLU 3.4 0.2 - - - -
12E GLN* 1.3 80.4 - - + +
14E GLU* 1.3 60.4 + - - +
16E VAL* 3.4 21.9 - - + +
17E ALA* 3.5 11.1 + - - +
221E GLN* 5.9 0.2 + - - -
224G VAL* 6.3 2.5 - - + -
227G GLY* 3.6 34.5 - - - +
228G ILE 4.0 14.6 - - - +
229G PRO* 4.1 18.6 - - + -
251G ARG* 4.8 7.6 - - - +
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Residues in contact with GLU 14 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E ALA 3.3 16.2 + - - +
11E GLU* 4.0 4.0 - - - +
13E LEU* 1.3 78.1 - - - +
15E LYS* 1.3 59.2 + - - +
17E ALA* 3.0 8.8 + - - +
18E GLU* 2.9 30.3 + - - +
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Residues in contact with LYS 15 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E GLU 3.0 20.5 + - - +
14E GLU* 1.3 78.3 - - - +
16E VAL* 1.3 59.9 + - - +
18E GLU* 3.3 28.6 - - - +
19E GLN* 3.6 15.4 + - - +
15G LYS 5.3 2.1 - - - +
19G GLN* 3.7 29.7 - - + +
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Residues in contact with VAL 16 (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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12E GLN* 3.1 17.6 + - + +
13E LEU* 3.4 20.4 - - + +
15E LYS* 1.3 74.6 - - - +
17E ALA* 1.3 65.3 + - + +
19E GLN* 3.4 9.5 + - - +
20E PHE* 3.0 29.3 - - + -
221E GLN* 4.7 9.6 - - + +
16G VAL* 4.8 15.9 - - + +
19G GLN* 3.8 24.2 - - + -
20G PHE* 4.3 7.2 - - + -
224G VAL* 4.2 39.3 - - + -
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Residues in contact with ALA 17 (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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13E LEU 3.5 11.0 + - - +
14E GLU* 3.0 11.8 + - - +
16E VAL* 1.3 78.4 - - + +
18E GLU* 1.3 65.7 + - - +
19E GLN 3.0 1.6 - - - -
20E PHE* 2.9 27.4 + - - +
21E PRO* 4.3 0.3 - - - +
217E LYS* 4.6 20.4 - - + -
218E THR* 5.2 4.6 - - + +
221E GLN* 4.6 8.1 - - - +
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Residues in contact with GLU 18 (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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14E GLU 2.9 13.1 + - - +
15E LYS* 3.3 24.9 - - - +
17E ALA* 1.3 74.4 - - - +
19E GLN* 1.3 73.7 + - - +
20E PHE 3.2 1.4 + - - -
21E PRO* 3.5 17.7 - - - +
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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