Contacts of the helix formed by residues 4 - 20 (chain A) in PDB entry 2YVE
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 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A THR* 1.3 91.4 + - - +
5A LYS* 1.3 64.2 + - - +
6A LYS* 3.6 10.3 + - - +
7A GLU* 3.0 24.9 + - - +
8A MET* 3.0 10.7 + - - +
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Residues in contact with LYS 5 (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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1A MET* 4.9 15.8 - - - +
3A THR 3.9 0.4 + - - -
4A SER* 1.3 70.6 - - - +
6A LYS* 1.3 66.3 + - - +
8A MET* 3.1 35.0 + - + +
9A ILE* 2.9 34.8 + - + +
36A LEU* 4.7 13.2 - - + +
44A HIS* 4.3 19.3 - - + +
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Residues in contact with LYS 6 (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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4A SER* 3.2 9.3 - - - +
5A LYS* 1.3 81.4 - - - +
7A GLU* 1.3 61.5 + - - +
9A ILE* 3.3 8.0 + - - +
10A LEU* 3.1 29.1 + - + +
44A HIS* 3.9 35.1 + - + +
45A PHE* 3.6 33.4 - - + -
54A GLY* 6.2 0.9 - - - -
2004A GOL 4.3 18.3 + - - -
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Residues in contact with GLU 7 (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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3A THR* 3.8 28.1 - - - +
4A SER* 3.0 22.8 + - - +
6A LYS* 1.3 72.9 - - - +
8A MET* 1.3 66.5 + - - +
10A LEU* 3.1 10.2 + - - +
11A ARG* 2.9 60.8 + - + +
58A LEU* 4.1 18.4 - - + +
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Residues in contact with MET 8 (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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3A THR* 3.8 8.8 + - - +
4A SER 3.0 13.2 + - - +
5A LYS* 3.1 45.8 - - + +
7A GLU* 1.3 75.8 - - - +
9A ILE* 1.3 75.3 + - + +
11A ARG* 3.3 7.9 + - + +
12A THR* 2.8 42.3 + - - +
34A THR* 4.6 13.7 - - - +
36A LEU* 4.3 12.3 - - + -
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Residues in contact with ILE 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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5A LYS* 2.9 19.7 + - + +
6A LYS* 3.5 7.2 - - - +
7A GLU 3.2 0.2 - - - -
8A MET* 1.3 85.0 - - + +
10A LEU* 1.3 59.3 + - - +
12A THR* 3.2 5.3 + - - -
13A ALA* 2.9 26.9 + - - +
30A LEU* 3.9 16.3 - - + +
34A THR* 4.5 2.5 - - + -
36A LEU* 3.6 31.6 - - + -
41A LEU* 3.8 23.6 - - + -
44A HIS* 3.5 38.8 - - + +
45A PHE* 3.8 16.4 - - + -
51A LEU* 4.7 1.1 - - + -
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Residues in contact with LEU 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 LYS* 3.1 27.2 + - + +
7A GLU* 3.1 9.8 + - - +
9A ILE* 1.3 77.3 - - - +
11A ARG* 1.3 56.7 + - - +
13A ALA* 3.2 4.6 + - - +
14A ILE* 2.9 34.6 + - - +
45A PHE* 3.4 34.1 - - + -
51A LEU* 3.8 14.8 - - + +
54A GLY* 3.8 24.2 - - - +
55A MET* 3.7 25.5 - - + +
58A LEU* 3.7 21.5 - - + -
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Residues in contact with ARG 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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3A THR* 6.0 1.3 - - + +
7A GLU* 2.9 49.3 + - + +
8A MET* 3.7 7.6 - - - +
10A LEU* 1.3 75.9 - - - +
12A THR* 1.3 57.9 + - - +
14A ILE* 3.4 10.3 + - - +
15A ASP* 3.0 36.6 + - - +
58A LEU* 3.6 23.7 - - + +
59A LEU* 4.8 7.3 - - - +
62A ASP* 2.7 43.4 + - - -
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Residues in contact with THR 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 MET* 2.8 34.1 + - - +
9A ILE 3.5 4.7 - - - -
11A ARG* 1.3 75.8 - - - +
13A ALA* 1.3 58.1 + - - +
15A ASP* 3.3 8.5 + - + +
16A TYR* 2.8 28.1 + - - +
30A LEU* 4.3 0.7 - - + -
33A ALA* 3.7 29.4 - - + +
34A THR* 3.5 27.1 - - + -
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Residues in contact with ALA 13 (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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9A ILE 2.9 13.8 + - - +
10A LEU* 3.5 10.1 - - - +
12A THR* 1.3 73.8 - - - +
14A ILE* 1.3 64.8 + - - +
16A TYR* 3.2 7.5 + - - +
17A ILE* 3.1 25.8 + - - +
25A LEU* 4.2 11.7 - - + +
30A LEU* 3.8 23.1 - - + +
51A LEU* 4.4 3.1 - - + -
55A MET* 3.7 24.0 - - + -
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Residues in contact with ILE 14 (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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10A LEU 2.9 25.7 + - - +
11A ARG* 3.7 12.8 - - - +
12A THR 3.3 0.2 - - - -
13A ALA* 1.3 76.0 - - - +
15A ASP* 1.3 66.8 + - - +
17A ILE* 3.2 10.6 + - - +
18A GLY 3.2 15.4 + - - -
55A MET* 3.7 26.9 - - + +
58A LEU* 4.3 15.5 - - + -
59A LEU* 4.0 36.1 - - + -
95A PRO* 3.5 22.7 - - + +
96A GLU 5.4 0.4 - - - +
99A LEU* 4.6 5.2 - - + -
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Residues in contact with ASP 15 (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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11A ARG* 3.0 24.7 + - - +
12A THR* 3.3 8.2 + - + +
14A ILE* 1.3 80.0 - - - +
16A TYR* 1.3 63.0 + - - +
18A GLY* 3.0 4.9 + - - +
19A GLU* 3.0 24.1 + - - +
95A PRO* 5.4 0.9 - - - -
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Residues in contact with TYR 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 THR 2.8 13.9 + - - +
13A ALA* 3.2 12.5 + - - +
15A ASP* 1.3 73.8 - - - +
17A ILE* 1.3 61.7 + - - +
19A GLU* 3.2 6.0 + - - +
20A TYR* 2.8 64.8 + + + +
21A SER 3.5 19.7 - - - -
24A THR* 2.8 28.2 + - - -
25A LEU* 3.6 32.8 - - + -
29A SER* 3.5 35.8 - - - -
30A LEU* 5.3 1.3 - - + -
33A ALA* 4.5 14.1 - - + -
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Residues in contact with ILE 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 ALA 3.1 9.5 + - - +
14A ILE* 3.2 8.3 + - - +
16A TYR* 1.3 75.7 - - - +
18A GLY* 1.3 60.9 + - - +
20A TYR 3.2 12.0 - - - -
21A SER 3.7 16.6 - - - +
22A LEU* 3.6 43.7 - - + +
25A LEU* 4.1 8.5 - - + -
55A MET* 3.7 27.4 - - + -
94A ARG* 2.9 18.7 + - - -
95A PRO* 3.9 20.6 - - + +
98A LEU* 4.1 16.4 - - + -
99A LEU* 4.3 15.5 - - + -
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Residues in contact with GLY 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 ILE 3.2 4.8 + - - -
15A ASP* 3.0 9.3 + - - -
17A ILE* 1.3 80.2 - - - +
19A GLU* 1.3 58.5 + - - +
94A ARG* 3.4 14.6 + - - +
95A PRO* 3.3 23.7 - - - +
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Residues in contact with GLU 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 ASP 3.0 14.1 + - - +
16A TYR* 3.9 3.9 - - - +
18A GLY* 1.3 76.7 - - - +
20A TYR* 1.3 99.8 + - + +
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Residues in contact with TYR 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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16A TYR* 2.8 54.6 + + + +
17A ILE 3.2 3.2 - - - +
19A GLU* 1.3 117.6 + - + +
21A SER* 1.3 65.0 + - - +
24A THR* 3.9 5.2 - - - +
94A ARG* 2.9 22.5 + - - -
23B GLU* 4.7 1.0 - - - +
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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