Contacts of the helix formed by residues 3 - 19 (chain A) in PDB entry 4G4Q
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 GLU 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 1.3 75.6 - - - +
4A LEU* 1.3 68.3 + - - +
5A PRO* 3.3 1.6 - - - -
6A GLU* 2.8 23.0 + - - +
7A VAL* 3.0 18.9 + - - +
60A LYS* 2.9 35.0 + - - +
173A GLY* 3.2 23.7 + - - -
174A ASN* 4.4 4.9 + - - +
175A ILE* 3.9 22.3 + - + +
176A TYR* 3.6 18.2 - - + +
9C A 4.6 9.0 + - - +
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Residues in contact with LEU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 1.3 72.5 + - - +
5A PRO* 1.3 72.8 - - + +
7A VAL* 3.0 6.2 + - - +
8A GLU* 2.9 20.3 + - + +
57A ARG* 3.6 37.8 - - - +
59A GLY 3.8 7.4 - - - +
60A LYS* 3.6 15.2 - - + +
137A GLU* 4.3 0.2 - - - +
138A PRO* 3.7 22.2 - - + -
139A LEU* 5.3 3.8 - - + -
170A ALA 3.4 25.4 - - - +
171A GLY 3.6 16.1 + - - +
176A TYR* 4.8 0.2 - - - -
211A ILE* 4.0 12.3 - - + -
215A VAL* 3.9 21.1 - - + -
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Residues in contact with PRO 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU 3.4 4.7 - - - -
4A LEU* 1.3 95.8 - - + +
6A GLU* 1.3 68.5 + - + +
8A GLU* 3.3 5.0 + - + +
9A THR* 3.1 23.7 + - - -
176A TYR* 3.4 22.0 - - + +
211A ILE* 4.0 12.1 - - + -
214A ALA* 3.4 49.1 - - + +
215A VAL* 3.8 17.5 - - + +
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Residues in contact with GLU 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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2A PRO* 3.7 18.9 - - + +
3A GLU* 2.8 40.0 + - - +
5A PRO* 1.3 88.0 - - + +
7A VAL* 1.3 65.6 + - - +
9A THR* 2.9 12.5 + - - -
10A ILE* 2.8 28.4 + - + +
176A TYR* 3.8 7.3 + - - -
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 4.1 21.8 - - + +
3A GLU 3.0 19.9 + - - +
4A LEU* 3.0 8.0 + - - +
6A GLU* 1.3 75.8 - - - +
8A GLU* 1.3 56.0 + - - +
10A ILE* 3.1 10.1 + - - +
11A ARG* 2.9 26.7 + - - +
57A ARG* 3.7 21.1 - - + -
60A LYS* 3.8 31.4 - - + +
62A LEU* 3.7 25.5 - - + +
75A LEU* 5.1 10.1 - - + -
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 2.9 12.4 + - + +
5A PRO* 3.6 11.0 - - + +
7A VAL* 1.3 76.1 - - - +
9A THR* 1.3 61.2 + - - +
11A ARG* 3.0 38.7 + - - +
12A ARG* 3.0 34.6 + - - +
57A ARG* 2.7 47.2 + - - +
215A VAL* 4.3 21.1 - - + +
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Residues in contact with THR 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 PRO 3.1 13.3 + - - -
6A GLU* 2.9 13.7 + - - -
8A GLU* 1.3 75.1 - - - +
10A ILE* 1.3 62.9 + - + +
12A ARG* 3.3 29.3 + - - +
13A THR* 2.9 39.8 + - + +
215A VAL 5.1 2.4 + - - -
217A LYS 4.6 10.2 + - - -
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Residues in contact with ILE 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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2A PRO* 4.4 10.8 - - + -
6A GLU* 2.8 21.6 + - + +
7A VAL* 3.4 14.1 - - - +
9A THR* 1.3 77.9 - - + +
11A ARG* 1.3 57.5 + - - +
13A THR* 3.8 6.1 - - - +
14A LEU* 2.8 52.3 + - + +
62A LEU* 4.0 20.9 - - + -
75A LEU* 3.7 26.7 - - + -
80A ARG* 5.6 3.4 - - + -
81A TYR* 4.7 14.1 - - + +
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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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7A VAL 2.9 16.0 + - - +
8A GLU* 3.0 41.5 + - - +
10A ILE* 1.3 74.5 - - - +
12A ARG* 1.3 85.7 + - - +
15A LEU* 3.3 39.1 + - - +
55A LEU* 3.1 52.3 + - + +
56A GLU* 3.8 5.8 - - - +
57A ARG* 3.7 20.0 - - + +
62A LEU* 3.9 8.5 - - + +
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Residues in contact with ARG 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 GLU* 3.0 24.0 + - - +
9A THR* 3.7 42.3 + - - +
11A ARG* 1.3 100.5 - - - +
13A THR* 1.3 66.5 + - + +
15A LEU* 4.3 1.9 - - - +
16A PRO* 3.3 22.5 - - - +
215A VAL* 5.1 8.5 + - - +
217A LYS 5.6 3.0 + - - -
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Residues in contact with THR 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 THR* 2.9 32.3 + - + +
10A ILE* 3.4 8.0 + - - +
12A ARG* 1.3 88.7 - - + +
14A LEU* 1.3 66.4 + - - +
16A PRO* 3.3 11.9 - - - +
17A LEU* 3.4 19.6 - - - +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 2.8 29.3 + - + +
13A THR* 1.3 79.2 + - - +
15A LEU* 1.3 65.3 + - - +
17A LEU* 2.9 24.9 + - + +
18A ILE* 3.3 13.5 + - + +
55A LEU* 3.9 11.0 - - + -
62A LEU* 5.0 0.2 - - + -
64A PHE* 3.9 29.6 - - + -
81A TYR* 3.8 31.0 - - + +
82A ALA* 5.3 0.2 - - - -
83A VAL* 3.7 31.9 - - + +
106A LEU* 3.8 9.9 - - + -
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Residues in contact with LEU 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* 3.3 33.5 + - - +
12A ARG 4.3 2.5 - - - +
14A LEU* 1.3 76.8 - - - +
16A PRO* 1.3 67.5 - - + +
18A ILE* 3.1 8.1 + - + +
19A VAL* 2.8 50.5 + - + +
52A VAL* 5.2 0.9 - - + -
54A GLY* 3.9 11.7 - - - -
55A LEU* 3.7 34.3 - - + +
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Residues in contact with PRO 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 ARG 3.3 21.5 - - - +
13A THR* 3.3 12.8 - - - +
15A LEU* 1.3 96.7 - - + +
17A LEU* 1.3 64.1 + - + +
18A ILE 3.4 0.5 + - - -
19A VAL* 4.1 18.8 + - + +
21A LYS* 5.8 0.5 - - - -
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Residues in contact with LEU 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 THR* 3.4 22.2 - - - +
14A LEU* 2.9 15.7 + - + +
16A PRO* 1.3 84.7 - - + +
18A ILE* 1.3 60.4 + - - +
21A LYS* 2.8 29.7 + - - -
83A VAL* 3.8 32.2 - - + +
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Residues in contact with ILE 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 LEU* 3.6 20.4 - - + +
15A LEU* 3.6 6.7 - - + +
17A LEU* 1.3 86.3 - - - +
19A VAL* 1.3 70.6 + - - +
20A GLY 3.4 0.5 + - - -
21A LYS* 3.1 25.9 + - - +
52A VAL* 3.5 25.9 - - + +
55A LEU* 4.5 8.1 - - + -
64A PHE* 3.6 38.1 - - + -
83A VAL* 3.7 21.8 - - + -
100A PHE* 4.0 25.1 - - + -
106A LEU* 4.4 10.5 - - + -
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Residues in contact with VAL 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 LEU* 2.8 31.1 + - + +
16A PRO* 4.1 17.5 - - + +
18A ILE* 1.3 77.7 - - - +
20A GLY* 1.3 63.6 + - - +
21A LYS* 3.2 8.1 + - - +
52A VAL* 3.8 12.3 - - - +
53A ARG* 3.8 25.1 - - - +
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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