Contacts of the helix formed by residues 16 - 25 (chain A) in PDB entry 1EFA
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 SER 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA* 3.8 4.5 - - - -
15A VAL* 1.3 79.1 - - - +
17A TYR* 1.3 66.5 + - - +
18A GLN* 3.3 9.3 + - - +
19A THR* 3.1 18.9 + - - -
20A VAL* 3.1 21.1 + - - +
6D G 3.0 37.0 + - - -
7D T 4.2 18.0 - - - +
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Residues in contact with TYR 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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6A LEU* 3.4 31.0 - - + +
7A TYR* 3.6 45.1 - + + -
10A ALA* 4.0 3.9 - - + +
16A SER* 1.3 77.5 - - - +
18A GLN* 1.3 79.9 + - + +
20A VAL* 3.7 0.6 + - - -
21A SER* 3.1 20.6 + - - -
7D T 3.8 27.1 - - + -
8D G 2.9 44.6 + - - -
9D A 4.3 6.0 + - - -
13E C 5.5 3.1 - + + -
14E T 3.8 20.2 - - + -
15E C 4.7 0.2 - - - -
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Residues in contact with GLN 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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16A SER* 3.1 7.7 + - - +
17A TYR* 1.3 90.3 - - + +
19A THR* 1.3 66.8 + - - +
21A SER* 3.0 26.5 + - - -
22A ARG* 2.9 56.3 + - - +
6D G 4.0 2.2 + - - +
7D T 4.0 16.4 - - + +
14E T 4.0 5.9 - - - +
15E C 2.7 43.7 - - - +
16E A 3.4 10.1 - - - +
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Residues in contact with THR 19 (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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15A VAL* 3.4 37.0 - - + +
16A SER* 3.1 9.9 + - - -
18A GLN* 1.3 79.8 - - - +
20A VAL* 1.3 63.8 + - - +
22A ARG* 3.2 18.4 + - - +
23A VAL* 3.0 25.7 + - + +
34A THR* 6.1 2.5 - - - -
38A VAL* 4.2 10.1 - - + -
5D T 4.2 16.4 - - - +
6D G 3.1 25.6 + - - -
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Residues in contact with VAL 20 (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 LEU* 3.3 39.3 - - + +
9A VAL* 3.7 31.2 - - + -
10A ALA 4.1 3.4 - - - +
15A VAL* 3.6 16.2 - - + -
16A SER 3.1 18.2 - - - +
17A TYR 3.8 2.5 - - - +
18A GLN 3.2 0.2 - - - -
19A THR* 1.3 75.2 - - - +
21A SER* 1.3 55.6 + - - +
23A VAL* 3.0 4.5 + - - +
24A VAL* 2.8 35.7 + - - +
38A VAL* 4.0 11.4 - - + -
42A MET* 3.8 18.2 - - + -
47A TYR* 4.9 0.2 - - + -
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Residues in contact with SER 21 (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 LEU* 4.2 5.5 - - - +
17A TYR 3.1 15.0 + - - -
18A GLN* 3.0 29.3 + - - -
20A VAL* 1.3 75.4 - - - +
22A ARG* 1.3 62.0 + - - +
24A VAL* 3.2 4.8 + - - +
25A ASN* 2.6 34.9 + - - +
14E T 2.5 38.2 + - - +
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Residues in contact with ARG 22 (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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18A GLN* 2.9 25.0 + - + +
19A THR* 3.2 40.6 + - - +
21A SER* 1.3 74.7 + - - +
23A VAL* 1.3 64.8 + - + +
25A ASN* 3.0 4.6 + - - -
26A GLN 2.9 4.2 + - - -
27A ALA* 2.7 39.8 + - - +
28A SER 4.9 5.8 + - - -
29A HIS 3.8 21.1 - - - -
30A VAL* 5.4 1.8 - - - +
5D T 3.4 35.3 + - - +
6D G 2.9 43.8 + - - -
17E C 5.2 0.2 - - - +
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Residues in contact with VAL 23 (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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19A THR* 3.0 20.6 - - + +
20A VAL 3.2 5.4 - - - +
22A ARG* 1.3 75.8 - - + +
24A VAL* 1.3 62.7 + - - +
26A GLN* 3.0 14.5 + - - +
27A ALA 5.0 0.4 - - - +
35A ARG* 4.2 14.8 - - - +
38A VAL* 3.7 35.0 - - + -
39A GLU* 3.5 35.9 - - + +
42A MET* 4.4 5.8 - - + -
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Residues in contact with VAL 24 (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 LEU* 4.3 4.0 - - + -
20A VAL* 2.8 25.3 + - + +
21A SER* 3.6 7.6 - - - +
23A VAL* 1.3 73.3 - - - +
25A ASN* 1.3 65.2 + - - +
26A GLN 3.3 2.6 + - - -
42A MET* 3.6 26.5 - - + -
47A TYR* 3.7 18.2 - - + +
49A PRO* 3.4 29.4 - - + -
54A GLN* 4.6 7.4 - - - +
14E T 5.1 0.9 - - - +
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Residues in contact with ASN 25 (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 SER* 2.6 39.3 + - - +
22A ARG* 3.8 4.0 - - - +
24A VAL* 1.3 79.6 - - - +
26A GLN* 1.3 65.2 + - - +
27A ALA* 3.0 5.1 + - - +
54A GLN* 4.4 1.5 + - - -
59A LYS* 4.1 18.7 - - - +
14E T 2.7 36.2 + - - +
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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