Contacts of the helix formed by residues 7 - 18 (chain A) in PDB entry 3ELW
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 THR 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A VAL* 1.3 83.1 - - + +
8A LEU* 1.3 62.7 + - - +
9A GLY 3.6 3.0 + - - -
10A GLU* 2.9 43.4 + - - +
11A VAL* 3.1 21.6 + - - +
187A TYR* 3.5 28.0 + - - +
189A PRO* 4.2 15.3 - - + -
234A ASN* 5.4 5.8 - - - -
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Residues in contact with LEU 8 (chain A).
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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6A VAL 4.0 0.6 + - - -
7A THR* 1.3 73.3 - - - +
9A GLY* 1.3 57.2 + - - +
11A VAL* 3.3 13.3 + - + +
12A TRP* 2.8 28.8 + - - +
234A ASN* 4.5 16.0 + - + +
237A SER* 3.8 13.9 - - - -
238A ARG* 3.7 42.0 - - + +
241A LEU* 3.9 21.4 - - + +
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Residues in contact with GLY 9 (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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7A THR* 3.2 3.8 + - - -
8A LEU* 1.3 77.7 - - - +
10A GLU* 1.3 57.7 + - - +
12A TRP* 3.3 12.1 + - - +
13A LYS* 3.0 25.3 + - - +
187A TYR* 3.6 23.8 - - - +
217A HIS* 3.9 8.1 - - - -
234A ASN* 5.6 0.4 + - - -
237A SER* 3.4 20.9 + - - -
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Residues in contact with GLU 10 (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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6A VAL* 3.5 20.6 + - - +
7A THR* 2.9 51.7 + - - +
9A GLY* 1.3 73.7 - - - +
11A VAL* 1.3 63.8 + - - +
13A LYS* 3.3 4.6 + - - +
14A ARG* 3.1 23.9 + - - +
154A PRO* 5.9 2.7 - - + -
187A TYR* 3.5 23.8 - - + -
188A HIS* 4.1 14.6 + - + +
189A PRO* 4.4 11.7 - - - +
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Residues in contact with VAL 11 (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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6A VAL* 5.1 9.4 - - - +
7A THR 3.1 15.0 + - - +
8A LEU* 3.4 18.2 - - + +
10A GLU* 1.3 75.7 - - - +
12A TRP* 1.3 62.4 + - - +
14A ARG* 3.3 11.8 + - - +
15A GLN* 3.0 49.0 + - + +
241A LEU* 4.4 9.4 - - + -
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Residues in contact with TRP 12 (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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8A LEU 2.8 17.0 + - - +
9A GLY* 3.3 17.5 + - - +
11A VAL* 1.3 73.3 - - - +
13A LYS* 1.3 93.3 + - + +
15A GLN* 3.3 3.5 + - - +
16A LEU* 2.9 40.5 + - + +
27A TYR* 3.0 29.0 + - - -
157A GLU* 5.5 2.2 - - - -
187A TYR* 4.2 4.5 - + - -
214A ASN 3.1 19.7 + - - -
215A SER 3.7 16.6 - - - -
216A THR* 3.6 6.3 - - - -
217A HIS* 3.4 44.0 - + + -
237A SER 4.9 2.9 - - - +
240A LEU* 3.5 26.0 - - + +
241A LEU* 3.7 19.7 - - + +
244A MET* 3.8 12.4 - - + +
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Residues in contact with LYS 13 (chain A).
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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9A GLY 3.0 12.7 + - - +
10A GLU* 3.7 6.1 - - - +
11A VAL 3.3 0.4 - - - -
12A TRP* 1.3 95.0 - - + +
14A ARG* 1.3 67.4 + - - +
16A LEU* 3.5 15.6 + - + +
17A ASN* 3.5 12.0 + - - +
151A SER 2.9 26.1 + - - -
152A SER 3.8 16.2 - - - +
154A PRO* 4.4 18.8 - - + -
157A GLU* 3.8 17.0 + - - +
187A TYR* 3.5 23.6 - - + +
215A SER 5.0 1.4 + - - -
4634A GP3 2.8 36.4 + - - +
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Residues in contact with ARG 14 (chain A).
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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10A GLU 3.1 15.9 + - - +
11A VAL* 3.6 10.7 + - - +
13A LYS* 1.3 75.3 - - - +
15A GLN* 1.3 72.4 + - - +
17A ASN* 3.4 15.7 + - - +
18A MET* 3.4 50.4 + - + +
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Residues in contact with GLN 15 (chain A).
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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11A VAL* 3.0 34.3 + - + +
12A TRP 3.7 1.8 - - - +
14A ARG* 1.3 85.9 + - + +
16A LEU* 1.3 64.9 + - - +
18A MET* 3.1 34.5 + - + +
19A LEU* 3.7 10.7 + - - +
241A LEU* 3.6 24.2 - - - +
244A MET* 3.7 21.6 - - - +
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Residues in contact with LEU 16 (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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12A TRP* 2.9 30.8 + - + +
13A LYS* 3.7 11.4 - - + +
14A ARG 3.4 0.2 - - - -
15A GLN* 1.3 76.6 - - - +
17A ASN* 1.3 59.1 - - - +
18A MET 3.3 1.0 + - - -
19A LEU* 3.3 12.4 + - + +
24A PHE* 3.7 26.9 - - + -
27A TYR* 3.7 33.4 - - + -
214A ASN 4.6 0.4 - - - +
215A SER* 3.4 28.7 - - - +
244A MET* 3.7 8.9 - - + +
4634A GP3 2.8 48.6 + - - +
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Residues in contact with ASN 17 (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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13A LYS 3.5 7.4 + - - +
14A ARG* 3.4 11.7 + - - +
15A GLN 3.2 0.8 - - - -
16A LEU* 1.3 77.1 - - - +
18A MET* 1.3 61.0 + - + +
19A LEU 3.2 2.1 + - - +
152A SER* 4.1 25.7 - - - +
4634A GP3 3.8 25.5 + - - +
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Residues in contact with MET 18 (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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14A ARG* 3.4 54.3 - - + +
15A GLN* 3.1 28.1 + - - +
17A ASN* 1.3 77.2 - - + +
19A LEU* 1.3 63.7 + - + +
20A GLY 3.5 2.4 + - - -
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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