Contacts of the helix formed by residues 11 - 23 (chain B) in PDB entry 4HH3
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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PRO* 6.2 3.1 - - + +
9B SER 4.3 1.0 + - - -
10B LEU* 1.3 75.6 - - - +
12B PRO* 1.3 75.9 - - + +
13B ASP* 4.6 4.7 - - + +
14B LEU* 3.1 17.3 + - + +
15B VAL* 3.0 18.9 + - - +
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Residues in contact with PRO 12 (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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7A LEU* 6.0 0.7 - - - +
8A PRO 6.0 1.8 - - - +
10B LEU 4.2 3.1 - - - +
11B ALA* 1.3 87.0 - - + +
13B ASP* 1.3 64.1 + - - +
15B VAL* 3.3 9.3 + - + +
16B ARG* 3.1 21.7 + - - +
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Residues in contact with ASP 13 (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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11B ALA* 3.3 3.7 - - + -
12B PRO* 1.3 82.0 - - - +
14B LEU* 1.3 63.5 + - - +
16B ARG* 3.4 17.3 + - - +
17B ASP* 3.1 21.7 + - - +
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Residues in contact with LEU 14 (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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80A GLY* 5.8 7.4 - - - +
105A HIS* 4.7 8.5 - - + +
106A ARG 5.3 2.7 - - - +
107A LEU* 4.3 8.3 - - + -
108A PRO* 3.7 33.2 - - + -
10B LEU* 3.9 23.8 - - + -
11B ALA* 3.1 22.0 + - + +
13B ASP* 1.3 76.9 - - - +
15B VAL* 1.3 68.1 + - - +
17B ASP* 3.0 9.9 + - + +
18B LEU* 2.9 51.8 + - + +
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Residues in contact with VAL 15 (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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7A LEU* 5.1 2.2 - - + -
10A LEU* 4.4 20.2 - - + -
15A VAL* 4.0 29.4 - - + +
18A LEU* 5.2 2.5 - - + -
19A ILE* 5.6 4.0 - - + -
10B LEU* 3.7 28.5 - - + +
11B ALA 3.0 14.7 + - - +
12B PRO* 3.3 9.8 + - + +
14B LEU* 1.3 74.8 - - - +
16B ARG* 1.3 63.6 + - - +
18B LEU* 3.3 9.2 + - - +
19B ILE* 3.1 39.3 + - + +
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Residues in contact with ARG 16 (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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7A LEU* 4.7 25.3 - - + +
12B PRO 3.1 13.0 + - - +
13B ASP* 3.4 19.9 + - - +
14B LEU 3.1 0.2 - - - -
15B VAL* 1.3 79.3 - - - +
17B ASP* 1.3 57.2 + - - +
19B ILE* 3.4 3.5 + - - +
20B ALA* 2.9 27.4 + - - +
37B GLU* 2.7 34.6 + - - +
38B VAL 5.8 0.4 + - - -
39B MET* 3.3 34.3 - - + +
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Residues in contact with ASP 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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80A GLY 5.0 4.4 - - - +
81A ARG* 4.8 5.5 - - - -
82A GLY 4.5 7.3 + - - -
105A HIS* 3.7 20.3 + - - -
13B ASP 3.1 9.6 + - - +
14B LEU* 3.0 15.6 + - + +
16B ARG* 1.3 77.4 - - - +
18B LEU* 1.3 67.1 + - - +
20B ALA* 4.2 7.3 - - - +
21B THR* 3.0 36.5 + - - +
39B MET* 6.0 0.7 - - - +
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Residues in contact with LEU 18 (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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19A ILE* 3.9 24.7 - - + -
105A HIS* 3.3 46.0 - - + +
107A LEU* 4.8 4.0 - - + -
114A LEU* 3.8 23.8 - - + -
116A LEU* 3.4 11.2 - - + +
10B LEU* 4.1 15.5 - - + -
14B LEU* 2.9 35.4 + - + +
15B VAL* 3.8 8.1 - - - +
17B ASP* 1.3 76.2 - - - +
19B ILE* 1.3 62.5 + - - +
21B THR* 3.2 5.9 + - - -
22B ALA* 3.0 27.8 + - - +
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Residues in contact with ILE 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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7A LEU* 4.0 26.5 - - + -
18A LEU* 4.1 22.7 - - + +
19A ILE* 5.2 4.5 - - + +
22A ALA* 4.4 13.5 - - + -
15B VAL* 3.1 29.3 + - + +
16B ARG* 3.7 3.8 - - - +
18B LEU* 1.3 77.9 - - + +
20B ALA* 1.3 63.5 + - - +
22B ALA 3.3 0.2 + - - -
23B ALA* 2.9 26.3 + - - +
26B SER* 3.7 15.0 - - - +
114B LEU* 4.0 16.8 - - + -
116B LEU* 3.6 26.5 - - + -
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Residues in contact with ALA 20 (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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16B ARG 2.9 18.6 + - - +
17B ASP* 3.8 13.7 - - - +
19B ILE* 1.3 78.8 - - - +
21B THR* 1.3 57.3 + - + +
23B ALA 3.0 17.8 - - - +
24B ASP 5.4 0.7 - - - +
26B SER* 5.0 2.9 - - - -
39B MET* 3.7 43.4 - - + +
40B ALA* 5.2 7.2 - - - +
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Residues in contact with THR 21 (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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82A GLY* 5.8 1.6 - - - +
103A ILE* 4.3 19.2 - - + +
105A HIS* 3.0 28.4 + - + -
116A LEU* 3.6 3.9 - - - +
118A ARG* 2.9 26.0 + - - -
17B ASP* 3.0 38.1 + - - +
18B LEU 3.2 6.8 + - - -
20B ALA* 1.3 77.0 - - + +
22B ALA* 1.3 60.7 + - - +
23B ALA 3.9 0.2 - - - -
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Residues in contact with ALA 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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19A ILE* 5.1 1.3 - - + +
22A ALA* 3.5 28.5 - - + -
23A ALA* 3.9 9.3 - - + +
116A LEU* 3.9 22.9 - - + -
117A GLY 5.4 0.5 - - - +
118A ARG* 3.2 11.7 + - - +
18B LEU 3.0 18.7 + - - +
21B THR* 1.3 78.9 + - - +
23B ALA* 1.3 59.0 + - - +
118B ARG* 3.0 26.2 + - - -
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Residues in contact with ALA 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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22A ALA* 3.8 15.5 - - + +
118A ARG* 3.2 8.9 + - - -
19B ILE* 2.9 11.5 + - + +
20B ALA 3.0 19.5 - - - +
22B ALA* 1.3 78.2 - - - +
24B ASP* 1.3 62.8 + - - +
25B ILE 4.0 2.5 - - - +
26B SER* 3.2 26.7 - - - +
116B LEU* 4.6 3.1 - - - -
117B GLY 3.6 17.9 - - - +
118B ARG* 3.8 3.6 - - - +
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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