Contacts of the helix formed by residues 120 - 128 (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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN* 3.2 21.4 + - - +
118A THR* 2.2 22.9 + - - +
119A PRO* 1.3 71.9 - - + +
121A VAL* 1.3 64.8 + - - +
122A HIS 3.2 1.6 - - - -
123A ALA* 2.9 17.5 + - - +
124A SER* 3.0 10.6 + - - -
33B VAL* 3.8 5.6 - - - +
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Residues in contact with VAL 121 (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* 3.4 15.8 - - + +
13A ALA* 4.7 2.7 - - + -
114A PRO 4.8 1.1 - - - +
115A ALA* 2.6 49.6 - - + +
116A GLU* 3.3 16.2 - - - +
118A THR* 2.5 45.8 + - + +
120A ALA* 1.3 73.1 - - - +
122A HIS* 1.3 69.3 + - - +
124A SER* 2.4 48.0 + - - +
125A LEU* 3.5 3.2 + - + +
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Residues in contact with HIS 122 (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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106A LEU* 3.4 38.9 - - + +
115A ALA* 4.1 20.5 - - + +
118A THR 3.9 2.0 + - - +
120A ALA 3.2 0.4 - - - -
121A VAL* 1.3 86.3 - - + +
123A ALA* 1.3 58.1 + - - +
124A SER 3.6 0.2 + - - -
125A LEU* 4.3 0.3 + - - +
126A ASP* 3.2 19.4 + - - +
30B ARG* 3.6 28.0 - - + +
33B VAL* 3.9 12.8 - - + -
34B VAL* 3.2 29.8 - - + +
109B VAL* 4.3 19.8 - - + +
112B CYS* 4.7 15.2 - - + +
113B VAL* 6.4 0.7 - - + -
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Residues in contact with ALA 123 (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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120A ALA* 2.9 11.5 + - - +
122A HIS* 1.3 77.6 - - - +
124A SER* 1.3 58.6 + - - +
126A ASP* 4.0 6.5 - - - -
127A LYS* 2.5 47.3 + - + +
33B VAL* 3.3 31.3 - - + +
34B VAL* 4.3 4.3 - - - +
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Residues in contact with SER 124 (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* 4.1 6.7 - - - +
9A ASN* 3.5 33.1 + - - +
10A VAL* 3.8 16.0 - - - +
13A ALA* 5.3 1.6 - - - +
120A ALA 3.0 5.5 + - - -
121A VAL* 2.4 42.4 + - - +
123A ALA* 1.3 71.5 - - - +
125A LEU* 1.3 60.4 + - - +
127A LYS* 4.3 4.7 - - - -
128A PHE* 2.6 42.9 + - - +
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Residues in contact with LEU 125 (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* 5.0 8.7 - - + -
13A ALA* 5.0 14.8 - - + -
14A TRP* 4.7 15.3 - - + -
66A LEU* 4.1 34.5 - - + -
102A SER 5.4 0.6 - - - +
105A LEU* 4.2 19.3 - - + -
106A LEU* 4.4 21.3 - - + -
109A LEU* 4.4 22.7 - - + -
114A PRO 5.5 5.2 - - - +
121A VAL* 3.5 3.2 + - + +
122A HIS 5.2 0.2 - - - +
124A SER* 1.3 85.6 + - - +
126A ASP* 1.3 58.5 + - - +
128A PHE* 4.3 4.3 - - + -
129A LEU* 3.1 34.2 + - + +
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A SER* 5.2 7.9 - - - +
103A HIS* 3.9 15.8 + - - -
106A LEU* 3.8 19.5 - - + +
122A HIS 3.2 21.5 + - - +
123A ALA* 3.9 2.0 - - - +
124A SER 3.1 0.6 - - - -
125A LEU* 1.3 81.6 - - - +
127A LYS* 1.3 62.1 + - + +
129A LEU* 3.7 17.1 - - - +
130A ALA 4.6 0.7 + - - -
34B VAL* 2.9 32.1 - - + +
35B TYR* 3.5 16.6 + - - -
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Residues in contact with LYS 127 (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* 3.5 29.4 - - + +
4A PRO* 5.8 0.2 - - - +
6A ASP* 3.0 40.6 + - + -
123A ALA* 2.5 36.9 + - + +
124A SER* 3.9 4.5 - - - +
126A ASP* 1.3 72.0 - - - +
128A PHE* 1.3 61.1 + - + +
129A LEU 2.6 4.9 + - - -
130A ALA* 2.4 46.6 + - + +
34B VAL 6.2 0.2 - - - +
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Residues in contact with PHE 128 (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* 3.4 22.0 - - + -
6A ASP 4.7 6.1 - - - +
7A LYS* 5.0 6.1 - - + -
10A VAL* 3.6 31.2 - - + -
11A LYS* 5.0 4.5 - - - -
66A LEU* 3.8 23.3 - - + -
69A ALA* 4.5 15.9 - - + -
70A VAL* 4.5 13.2 - - + -
73A VAL* 4.1 22.2 - - + -
76A MET* 4.7 0.4 - - + -
124A SER* 2.6 26.7 + - - +
125A LEU* 4.5 4.0 - - + -
127A LYS* 1.3 83.0 - - + +
129A LEU* 1.3 58.9 + - + +
130A ALA 2.9 0.8 + - - -
131A SER* 2.9 24.7 + - - -
132A VAL* 3.4 26.3 - - + +
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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