Contacts of the helix formed by residues 5 - 18 (chain A) in PDB entry 2H35
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 ALA 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PRO* 1.3 70.6 - - - +
6A ASP* 1.3 54.0 + - - +
7A LYS 2.5 20.9 + - - -
8A THR* 2.6 29.3 + - - +
9A ASN* 3.2 18.8 + - - +
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Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 5.1 7.6 - - + -
3A SER 5.4 0.9 - - - +
4A PRO* 2.9 29.2 + - + +
5A ALA* 1.3 78.0 + - - +
7A LYS* 1.3 59.4 + - + +
9A ASN* 3.8 9.1 + - - +
10A VAL* 3.4 22.3 + - - +
124A SER* 4.1 7.0 - - - +
127A LYS* 3.0 46.3 + - + +
128A PHE* 4.7 2.9 - - + +
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Residues in contact with LYS 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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2A LEU* 4.9 3.1 + - + -
3A SER* 3.2 39.7 + - - +
4A PRO 2.8 16.2 - - - +
5A ALA* 2.5 4.8 + - - -
6A ASP* 1.3 70.6 - - - +
8A THR* 1.3 60.9 + - - +
9A ASN 2.8 2.5 - - - -
10A VAL* 2.4 32.1 + - - -
11A LYS* 2.7 38.5 + - + +
73A VAL* 4.4 30.8 + - - +
128A PHE* 5.0 7.2 - - + -
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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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5A ALA* 2.6 27.3 + - + +
7A LYS* 1.3 78.0 - - - +
9A ASN* 1.3 59.1 + - - +
11A LYS* 3.7 10.2 - - - +
12A ALA* 3.0 29.0 + - + +
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Residues in contact with ASN 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 ALA* 3.2 19.1 + - - +
6A ASP* 4.0 5.4 - - - +
7A LYS 2.6 4.2 + - - -
8A THR* 1.3 81.2 - - - +
10A VAL* 1.3 59.7 + - - +
12A ALA* 3.6 5.1 - - - +
13A ALA* 3.1 27.5 + - - +
118A THR* 3.8 7.9 + - - +
120A ALA* 3.2 33.6 - - - +
121A VAL* 3.4 16.4 - - + +
124A SER* 3.5 24.5 + - - +
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Residues in contact with VAL 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 ASP 3.4 15.7 - - - +
7A LYS* 2.4 25.5 + - - +
9A ASN* 1.3 66.3 - - - +
11A LYS* 1.3 69.1 + - + +
12A ALA 3.0 1.5 + - - -
13A ALA* 3.2 5.4 + - - +
14A TRP* 2.8 30.6 + - + +
66A LEU* 5.3 6.5 - - + -
70A VAL* 4.0 25.4 - - + -
124A SER* 3.8 15.9 - - - +
125A LEU* 4.6 8.7 - - + +
128A PHE* 3.6 41.1 - - + -
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Residues in contact with LYS 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 LYS* 2.7 48.4 + - + +
8A THR* 3.7 9.2 - - - +
10A VAL* 1.3 74.7 - - + +
12A ALA* 1.3 55.1 + - - +
14A TRP* 3.2 9.5 + - - +
15A GLY* 2.8 25.3 + - - -
70A VAL* 3.2 49.8 + - + +
73A VAL* 4.3 14.1 - - - +
128A PHE* 5.0 2.8 - - - -
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Residues in contact with ALA 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* 3.0 23.8 + - + +
9A ASN* 3.6 7.2 - - - +
10A VAL 3.0 0.2 - - - -
11A LYS* 1.3 77.4 - - - +
13A ALA* 1.3 55.9 + - - +
15A GLY* 2.6 27.4 + - - -
16A LYS* 3.3 21.4 + - - +
116A GLU* 4.6 8.3 - - - +
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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 ASN 3.1 14.2 + - - +
10A VAL* 3.7 5.4 - - + +
12A ALA* 1.3 80.1 - - - +
14A TRP* 1.3 65.1 + - + +
16A LYS* 3.5 4.4 + - - +
17A VAL* 3.2 28.5 + - + +
113A LEU* 4.6 4.4 - - + +
114A PRO 5.4 2.5 - - - +
116A GLU* 3.0 30.0 + - - +
121A VAL* 4.7 4.9 - - + -
124A SER* 5.3 1.6 - - - +
125A LEU* 5.0 16.4 - - + -
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Residues in contact with TRP 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 VAL* 2.8 26.6 + - + +
11A LYS* 3.4 10.3 - - - +
12A ALA 3.0 0.2 - - - -
13A ALA* 1.3 82.2 - - + +
15A GLY* 1.3 58.0 + - - +
17A VAL* 3.9 21.3 - - + -
18A GLY* 3.0 24.5 + - - -
21A ALA* 3.9 16.2 - - + +
62A VAL* 6.1 0.2 - - + -
63A ALA* 3.4 33.0 - - + -
66A LEU* 3.5 39.0 - - + -
67A THR* 2.6 32.0 + - + +
70A VAL* 5.1 13.2 - - + -
105A LEU* 5.7 6.7 - - + -
109A LEU* 6.0 1.6 - - + -
125A LEU* 4.7 17.5 - - + -
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Residues in contact with GLY 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 LYS 2.8 8.8 + - - -
12A ALA* 2.6 18.8 + - - -
14A TRP* 1.3 71.3 - - - +
16A LYS* 1.3 67.2 + - - +
17A VAL 3.4 0.3 + - - -
18A GLY* 3.7 8.4 + - - -
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Residues in contact with LYS 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 ALA* 3.3 25.2 + - - +
13A ALA* 4.1 5.8 - - - +
15A GLY* 1.3 76.9 - - - +
17A VAL* 1.3 69.8 + - - +
20A HIS* 4.7 4.2 - - - -
24A TYR* 5.2 1.6 + - - -
113A LEU* 3.6 33.1 - - + +
116A GLU* 4.1 13.9 + - - +
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Residues in contact with VAL 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* 3.2 20.0 + - + +
14A TRP* 3.8 23.6 - - + +
16A LYS* 1.3 83.4 - - - +
18A GLY* 1.3 67.3 + - - +
20A HIS* 3.1 24.8 + - - +
21A ALA* 3.1 46.7 - - + +
24A TYR* 3.7 25.6 - - + -
109A LEU* 4.6 5.2 - - + -
113A LEU* 4.1 14.6 - - + +
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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 TRP* 3.0 14.7 + - - -
15A GLY 4.1 7.0 - - - -
16A LYS 3.5 0.8 - - - -
17A VAL* 1.3 77.2 - - - +
19A ALA* 1.3 53.3 + - - -
20A HIS 2.5 17.0 + - - -
21A ALA* 3.1 15.1 + - - +
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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