Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 2F8A
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 HIS 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.7 1.1 - - + -
18A SER 2.9 33.2 + - - -
19A ALA* 3.9 16.0 - - + +
74A PHE* 5.3 2.9 - + - -
113A CYS* 4.0 27.4 - - + -
114A GLU 2.8 17.9 + - - +
119A GLY 3.4 2.4 + - - -
120A ALA* 1.3 73.1 - - - +
122A PRO* 1.3 82.2 - - + +
123A LEU* 3.0 42.2 + - + +
124A PHE* 2.9 22.0 + + + +
125A ALA 3.1 7.8 + - - -
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Residues in contact with PRO 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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17A PHE* 3.8 24.5 - - + -
120A ALA 3.4 6.5 - - - +
121A HIS* 1.3 100.6 - - + +
123A LEU* 1.3 61.5 + - - +
125A ALA* 3.8 9.0 - - + +
126A PHE* 3.0 24.8 + - - +
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Residues in contact with LEU 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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14A VAL* 4.1 16.8 - - + -
17A PHE* 3.9 30.6 - - + -
30A LEU* 3.9 26.0 - - + -
40A ILE* 4.4 9.9 - - + -
74A PHE* 3.5 38.4 - - + -
121A HIS* 3.0 23.1 + - + +
122A PRO* 1.3 76.8 - - - +
124A PHE* 1.3 67.0 + - + +
126A PHE* 3.4 2.5 + - + +
127A LEU* 2.9 46.6 + - + +
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Residues in contact with PHE 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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40A ILE* 3.8 15.9 - - + -
42A ASN* 4.5 13.5 - - + -
74A PHE* 3.5 50.5 - + + -
113A CYS* 4.6 1.1 - - - -
115A VAL* 3.6 48.9 - - + +
121A HIS* 2.9 20.7 + - + +
123A LEU* 1.3 84.5 - - + +
125A ALA* 1.3 66.2 + - - +
126A PHE 3.1 1.3 - - - -
127A LEU* 4.0 9.6 - - + +
128A ARG* 2.9 32.3 + - + +
158A VAL* 4.7 5.2 - - + -
165A PHE* 4.1 26.2 - + - -
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Residues in contact with ALA 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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115A VAL 4.6 0.4 + - - -
120A ALA* 4.6 8.3 - - + +
121A HIS 3.1 11.2 + - - +
122A PRO* 3.8 12.1 - - + +
124A PHE* 1.3 77.0 - - - +
126A PHE* 1.3 62.0 + - - +
128A ARG* 3.9 21.2 - - - +
129A GLU* 3.2 36.2 + - - +
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Residues in contact with PHE 126 (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 GLN* 3.3 43.3 - - + -
13A SER* 3.8 8.3 - - - -
14A VAL* 3.7 23.8 - - + -
17A PHE* 3.5 28.3 - + + -
122A PRO 3.0 17.8 + - - +
123A LEU* 3.5 5.8 - - + +
125A ALA* 1.3 74.9 - - - +
127A LEU* 1.3 69.2 + - + +
129A GLU* 3.2 8.7 + - + +
130A ALA* 2.9 29.2 + - + +
173A PRO* 3.5 33.9 - - + -
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Residues in contact with LEU 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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14A VAL* 4.0 15.3 - - + -
40A ILE* 4.1 20.9 - - + -
123A LEU* 2.9 39.3 + - + +
124A PHE* 3.4 14.1 + - + +
126A PHE* 1.3 78.1 - - + +
128A ARG* 1.3 57.8 + - - +
130A ALA* 3.3 3.5 + - - +
131A LEU* 3.0 33.6 + - - +
165A PHE* 3.8 42.4 - - + -
167A VAL* 4.5 5.2 - - + -
173A PRO* 3.9 29.2 - - + -
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Residues in contact with ARG 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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115A VAL 3.0 29.2 + - - -
116A ASN* 3.6 19.1 - - - +
117A GLY 4.2 5.1 + - - +
120A ALA* 4.0 7.9 - - - +
124A PHE* 2.9 17.5 + - - +
125A ALA* 3.9 20.7 + - - +
127A LEU* 1.3 77.7 - - - +
129A GLU* 1.3 59.0 + - - +
131A LEU 3.3 0.3 - - - +
132A PRO* 3.1 30.0 - - - +
154A CYS* 4.0 13.7 - - - +
156A ASN* 2.9 52.2 + - - +
157A ASP* 3.2 20.1 + - - -
158A VAL* 4.1 17.0 - - + +
165A PHE* 4.9 3.6 - - + -
176A ARG* 4.1 9.6 - - - +
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Residues in contact with GLU 129 (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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125A ALA* 3.2 25.3 + - - +
126A PHE* 3.2 6.4 + - + +
128A ARG* 1.3 79.1 - - - +
130A ALA* 1.3 63.1 + - - +
132A PRO* 3.9 12.2 - - - +
156A ASN* 4.1 16.4 - - - +
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Residues in contact with ALA 130 (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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126A PHE* 2.9 26.7 + - + +
127A LEU 3.3 4.5 + - - +
129A GLU* 1.3 77.7 - - - +
131A LEU* 1.3 67.0 + - + +
132A PRO* 3.6 6.7 - - - +
173A PRO* 3.9 30.7 - - + +
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Residues in contact with LEU 131 (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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127A LEU 3.0 10.7 + - - +
128A ARG 3.3 3.2 - - - +
130A ALA* 1.3 83.6 - - + +
132A PRO* 1.3 63.0 - - - +
133A ALA 3.2 6.0 + - - +
165A PHE* 4.1 16.2 - - + -
166A LEU 4.7 1.3 - - - +
173A PRO* 3.5 35.0 - - + +
174A LEU 3.8 21.5 - - - +
175A ARG* 3.7 31.4 - - - +
176A ARG* 2.8 37.9 + - + +
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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