Contacts of the helix formed by residues 2 - 18 (chain A) in PDB entry 1PJJ
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 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 1.3 75.2 - - - -
3A LEU* 1.3 68.1 + - - +
4A PRO 3.3 1.6 - - - -
5A GLU* 3.0 17.5 + - - +
6A VAL* 3.1 21.4 + - - +
57A LYS* 4.1 4.9 - - - -
168A GLY 3.7 7.6 - - - +
170A GLY* 2.8 36.3 + - - -
171A ASN 3.6 1.8 + - - -
172A ILE* 3.0 34.2 + - - +
173A TYR* 2.9 40.8 + - + +
7D 3DR 3.3 24.8 + - - +
8D T 3.5 1.1 - - - +
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Residues in contact with LEU 3 (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 GLU* 1.3 71.8 - - - +
4A PRO* 1.3 69.0 - - + +
6A VAL* 3.2 3.4 + - - +
7A GLU* 2.8 32.1 + - - +
54A ARG* 3.4 35.6 - - - +
56A GLY* 3.9 12.3 - - - +
57A LYS* 3.8 4.3 - - - +
134A GLU* 3.7 2.0 - - - +
135A PRO* 3.6 37.5 - - + -
167A ALA 3.7 11.2 - - - +
168A GLY* 3.1 22.2 + - - +
208A LEU* 5.0 5.2 - - + -
212A ILE* 3.7 27.8 - - + -
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Residues in contact with PRO 4 (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 GLU* 3.4 4.5 - - + -
3A LEU* 1.3 96.4 - - + +
5A GLU* 1.3 65.7 + - - +
7A GLU* 3.5 1.9 + - - +
8A THR* 2.8 32.6 + - - -
173A TYR* 3.5 18.6 - - + -
208A LEU* 3.6 24.5 - - + +
211A ALA* 3.5 42.8 - - + +
212A ILE* 3.9 13.7 - - + +
216A GLY* 4.3 1.5 + - - -
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Residues in contact with GLU 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 GLY* 4.2 11.0 - - - -
2A GLU* 3.0 37.9 + - - +
4A PRO* 1.3 73.2 - - - +
6A VAL* 1.3 65.8 + - + +
8A THR* 3.2 8.0 + - - -
9A VAL* 3.0 28.6 + - + +
73A LEU* 5.7 2.7 - - + -
172A ILE* 6.2 1.8 - - - -
173A TYR* 2.6 33.2 + - - -
215A GLY 5.4 0.2 - - - -
216A GLY* 3.4 5.9 - - - -
217A SER* 2.7 34.9 + - - +
226A GLY* 5.5 6.3 - - - +
7D 3DR 5.9 1.5 - - - +
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Residues in contact with VAL 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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1A GLY 4.0 15.5 - - - +
2A GLU 3.1 16.2 + - - +
3A LEU 3.7 6.1 - - - +
5A GLU* 1.3 73.6 - - - +
7A GLU* 1.3 60.4 + - - +
9A VAL* 3.2 7.8 + - - +
10A ARG* 2.8 26.7 + - - +
54A ARG* 3.7 21.5 - - + -
57A LYS* 3.5 32.5 - - - +
58A TYR 4.3 0.2 - - - -
59A LEU* 3.7 26.4 - - + +
73A LEU* 4.4 18.2 - - + -
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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 LEU 2.8 18.1 + - - +
4A PRO 3.7 4.7 - - - +
6A VAL* 1.3 75.8 - - - +
8A THR* 1.3 57.7 + - - +
10A ARG* 3.1 35.2 + - - +
11A ARG* 2.8 63.0 + - - +
54A ARG* 2.7 41.2 + - - +
212A ILE* 3.9 28.7 - - + -
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Residues in contact with THR 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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4A PRO 2.8 18.9 + - - -
5A GLU* 3.4 10.8 - - - -
7A GLU* 1.3 77.5 - - - +
9A VAL* 1.3 61.9 + - - +
11A ARG* 3.4 10.5 + - - +
12A GLU* 3.2 41.0 + - + +
212A ILE* 4.4 5.9 + - - -
215A GLY* 3.3 38.2 - - - +
216A GLY 3.7 0.3 + - - -
226A GLY* 3.6 16.6 - - - -
228A THR* 6.2 0.2 - - - +
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Residues in contact with VAL 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 GLU* 3.0 15.4 + - + +
6A VAL* 3.6 9.9 - - - +
8A THR* 1.3 75.4 - - - +
10A ARG* 1.3 64.9 + - - +
12A GLU* 3.2 6.2 + - - +
13A LEU* 2.9 44.6 + - + +
59A LEU* 4.0 15.7 - - + -
73A LEU* 4.9 11.7 - - + -
79A TYR* 4.2 15.3 - - + +
225A LEU* 3.9 34.3 - - + +
226A GLY* 4.5 3.8 - - - +
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Residues in contact with ARG 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 2.8 14.2 + - - +
7A GLU* 3.1 44.8 + - - +
9A VAL* 1.3 77.5 - - - +
11A ARG* 1.3 72.0 + - - +
13A LEU* 3.4 2.6 + - - +
14A GLU* 2.8 70.0 + - - +
52A ILE* 2.9 40.7 + - + +
53A SER* 3.6 20.8 - - - +
54A ARG* 3.7 6.5 - - + +
59A LEU* 3.7 13.4 - - + +
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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 GLU* 2.8 46.8 + - - +
8A THR* 3.7 8.3 - - - +
10A ARG* 1.3 86.2 - - - +
12A GLU* 1.3 67.5 + - + +
14A GLU* 3.4 9.2 + - - +
15A LYS* 3.1 24.5 + - - +
209A GLN* 5.8 1.0 + - - -
212A ILE* 3.4 39.6 + - - +
213A LYS* 5.4 2.6 - - - +
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Residues in contact with GLU 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 THR* 3.2 18.6 + - + +
9A VAL* 3.7 7.2 - - - +
11A ARG* 1.3 77.1 - - + +
13A LEU* 1.3 63.0 + - - +
15A LYS* 3.3 8.9 + - + +
16A ARG* 3.0 37.6 + - - +
225A LEU* 3.3 27.8 - - + +
226A GLY* 2.9 39.1 + - - -
228A THR* 4.9 6.9 + - - -
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Residues in contact with LEU 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 VAL* 2.9 36.3 + - + +
10A ARG* 3.8 3.8 - - - +
12A GLU* 1.3 76.2 - - - +
14A GLU* 1.3 58.6 + - - +
16A ARG* 4.4 1.8 - - - +
17A ILE* 2.8 60.1 + - + +
18A VAL 3.8 0.2 + - - -
52A ILE* 4.0 16.6 - - + -
59A LEU* 4.4 7.4 - - + -
61A PHE* 3.8 28.5 - - + -
79A TYR* 4.9 2.9 - - + -
81A LEU* 4.9 2.5 - - + -
103A LEU* 3.8 17.0 - - + -
225A LEU* 3.3 26.2 - - + -
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Residues in contact with GLU 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 ARG* 2.8 54.0 + - - +
11A ARG* 3.6 8.2 - - - +
13A LEU* 1.3 77.2 - - - +
15A LYS* 1.3 62.5 + - - +
18A VAL* 3.2 37.4 - - + +
51A GLY* 5.9 0.6 - - - -
52A ILE* 3.9 13.5 + - + +
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Residues in contact with LYS 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 3.1 17.6 + - - +
12A GLU* 3.6 8.7 - - + +
13A LEU 3.2 0.2 - - - -
14A GLU* 1.3 79.4 - - + +
16A ARG* 1.3 77.8 + - + +
18A VAL 5.3 0.2 - - - -
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Residues in contact with ARG 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 GLU* 3.0 23.3 + - - +
13A LEU 4.9 0.2 - - - -
15A LYS* 1.3 104.9 - - - +
17A ILE* 1.3 62.4 + - - +
18A VAL 3.7 2.4 - - - +
20A GLN* 4.1 4.2 + - - +
81A LEU* 3.4 38.8 + - + +
225A LEU* 4.0 16.2 - - - +
1002A GOL 3.0 44.4 + - - +
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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 LEU* 2.8 45.2 + - + +
16A ARG* 1.3 76.7 - - + +
18A VAL* 1.3 67.8 + - - +
19A GLY 3.2 0.3 + - - -
20A GLN* 3.0 28.1 + - + +
49A ILE* 3.5 37.9 - - + +
52A ILE* 4.1 7.2 - - + -
61A PHE* 4.0 19.1 - - + -
81A LEU* 3.8 33.9 - - + -
98A PHE* 4.0 12.3 - - + -
103A LEU* 4.1 7.0 - - + -
1002A GOL 4.2 3.4 - - - +
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Residues in contact with VAL 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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13A LEU 4.3 0.7 - - - +
14A GLU* 3.2 40.5 + - + +
16A ARG 3.7 2.7 - - - +
17A ILE* 1.3 76.2 - - - +
19A GLY* 1.3 63.0 + - - +
20A GLN* 3.3 3.3 + - - +
49A ILE* 3.7 6.3 - - + +
50A GLN* 3.4 22.9 - - - +
51A GLY* 3.8 24.5 - - - -
52A ILE* 4.5 2.9 - - + -
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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