Contacts of the helix formed by residues 16 - 25 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 3.8 6.5 - - - -
15B VAL* 1.3 78.0 - - - +
17B TYR* 1.3 67.7 + - - +
18B GLN* 3.3 8.8 + - - +
19B THR* 3.3 17.2 + - - -
20B VAL* 3.3 19.6 + - - +
6E G 2.5 43.6 + - - -
7E T 4.2 15.2 - - - +
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.2 34.2 - - + +
7B TYR* 3.2 48.2 - + + -
10B ALA* 4.0 3.2 - - - +
16B SER* 1.3 76.4 - - - +
18B GLN* 1.3 77.2 + - + +
20B VAL 3.6 0.5 + - - -
21B SER* 3.0 21.3 + - - -
13D C 5.8 2.7 - + + -
14D T 3.9 19.7 - - + -
15D C 4.7 0.7 - - - -
7E T 3.5 37.9 - - + -
8E G 3.1 39.7 + - - -
9E A 4.7 3.8 + - - -
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 3.2 3.0 + - - +
17B TYR* 1.3 85.8 - - + +
19B THR* 1.3 60.4 + - - +
21B SER* 3.0 23.4 + - - -
22B ARG* 2.8 65.4 + - - +
14D T 4.1 5.5 - - - +
15D C 2.7 42.5 + - - +
16D A 2.9 15.8 + - - +
6E G 3.6 6.2 + - - +
7E T 3.9 20.0 - - + +
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.5 37.6 - - + +
16B SER* 3.3 4.3 + - - -
18B GLN* 1.3 76.7 - - - +
20B VAL* 1.3 64.7 + - - +
22B ARG* 3.2 20.3 + - + +
23B VAL* 3.1 27.6 + - + +
30B VAL* 5.7 2.0 - - + -
34B THR* 4.1 16.6 - - + -
38B VAL* 4.2 6.1 - - + -
5E T 3.8 18.1 - - - +
6E G 3.1 24.9 + - - -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.3 36.3 - - + +
9B VAL* 4.1 20.4 - - + -
10B ALA 4.1 3.4 - - - +
15B VAL* 3.7 17.9 - - + -
16B SER 3.3 15.7 - - - +
17B TYR 3.7 5.8 - - - +
19B THR* 1.3 72.2 - - - +
21B SER* 1.3 62.0 + - - +
23B VAL* 3.1 2.6 + - - +
24B VAL* 2.8 33.7 + - + +
38B VAL* 4.1 10.3 - - + -
42B MET* 3.3 27.8 - - + -
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.1 5.1 - - - +
17B TYR 3.0 14.9 + - - -
18B GLN* 3.0 26.9 + - - -
20B VAL* 1.3 75.6 - - - +
22B ARG* 1.3 62.7 + - - +
24B VAL* 3.2 6.5 + - - +
25B ASN* 2.9 32.5 + - - +
14D T 2.5 40.4 + - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLN* 2.8 36.3 + - + +
19B THR* 3.3 30.8 + - + +
21B SER* 1.3 72.7 - - - +
23B VAL* 1.3 61.7 + - + +
25B ASN* 3.1 2.9 + - - -
26B GLN 3.0 3.6 + - - -
27B ALA* 2.6 52.6 + - + +
28B SER 4.8 3.7 + - - -
29B HIS 4.0 18.4 - - - -
30B VAL* 4.8 7.9 - - + +
17D C 4.7 1.4 - - - +
5E T 3.1 46.9 + - - +
6E G 3.0 36.4 + - - -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 3.2 17.0 - - + +
20B VAL 3.1 6.2 + - - +
22B ARG* 1.3 75.6 - - + +
24B VAL* 1.3 63.9 + - - +
26B GLN* 3.1 18.6 + - - +
27B ALA 4.9 0.4 - - - +
30B VAL* 4.3 14.4 - - + -
35B ARG* 4.1 24.9 - - + +
38B VAL* 3.9 30.3 - - + -
39B GLU* 3.5 35.5 - - + +
42B MET* 4.8 4.5 - - + -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.2 5.8 - - + -
20B VAL* 2.8 33.1 + - + +
21B SER* 3.5 6.5 - - - +
23B VAL* 1.3 73.5 - - - +
25B ASN* 1.3 66.3 + - - +
26B GLN* 3.2 9.2 + - - -
42B MET* 3.8 24.2 - - + -
47B TYR* 4.1 12.3 - - + +
49B PRO* 3.9 27.1 - - + -
54B GLN* 4.7 7.6 - - - +
14D T 4.9 2.2 - - - +
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 2.9 24.2 + - - +
22B ARG* 3.9 3.1 - - - +
24B VAL* 1.3 80.6 - - - +
26B GLN* 1.3 71.0 + - - +
27B ALA* 3.0 6.6 + - + +
54B GLN* 4.6 1.2 + - - -
59B LYS* 4.5 15.7 - - - +
14D T 2.9 41.7 + - - -
15D C 5.2 5.1 + - - -
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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