Contacts of the helix formed by residues 118 - 131 (chain A) in PDB entry 4AF3
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 VAL 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.4 29.9 + - + +
116A GLU* 3.2 31.4 - - + +
117A GLY* 1.3 73.9 - - - +
119A GLU* 1.3 66.5 + - - +
120A HIS 3.2 4.4 + - - +
121A GLN* 3.3 27.3 + - + +
122A LEU* 3.3 21.5 + - + +
220A GLY 5.4 10.3 - - - +
245A ILE 6.0 0.9 - - - -
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Residues in contact with GLU 119 (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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113A ILE* 3.6 19.5 - - + +
114A GLU* 3.7 28.7 - - - +
117A GLY* 3.2 9.3 - - - -
118A VAL* 1.3 85.1 + - - +
120A HIS* 1.3 63.3 + - + +
122A LEU* 3.9 4.5 + - - +
123A ARG 3.3 12.5 + - - -
877D LEU* 3.2 41.1 - - + +
881D PHE* 3.9 25.9 - - + +
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.2 0.8 - - - +
119A GLU* 1.3 82.2 - - + +
121A GLN* 1.3 66.1 + - - +
123A ARG* 3.3 28.1 + - - +
124A ARG* 3.2 25.1 + - - +
245A ILE* 3.7 37.8 - - + +
246A GLU* 4.0 10.4 - - + +
877D LEU* 3.6 24.6 - - + +
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.3 29.6 + - + +
120A HIS* 1.3 76.7 - - - +
122A LEU* 1.3 52.2 - - - +
124A ARG* 3.0 3.6 + - - +
125A GLU* 2.5 38.7 + - - +
220A GLY 4.0 22.3 - - - +
245A ILE 4.0 6.0 + - - +
246A GLU 3.8 9.0 - - - -
247A GLY* 3.5 31.3 + - - +
248A ARG* 3.8 16.5 + - - +
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Residues in contact with LEU 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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108A LEU* 3.8 24.7 - - + -
113A ILE* 3.9 30.5 - - + -
118A VAL* 3.3 15.1 + - + +
119A GLU* 3.9 4.3 - - - +
121A GLN* 1.3 76.7 - - - +
123A ARG* 1.3 67.6 + - - +
125A GLU* 3.6 5.7 - - - +
126A ILE* 2.8 40.9 + - + +
150A ILE* 4.7 16.4 - - + -
152A LEU* 5.0 2.7 - - + -
219A PHE* 4.8 16.2 - - + -
875D LEU* 3.7 20.2 - - + -
881D PHE* 5.1 4.9 - - + -
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU 3.3 17.4 + - - +
120A HIS* 3.3 36.8 + - - +
122A LEU* 1.3 80.7 - - - +
124A ARG* 1.3 74.9 + - - +
126A ILE* 3.4 5.0 + - - +
127A GLU* 3.2 29.7 + - - +
246A GLU* 2.6 34.8 + - - +
874D PRO* 6.0 2.2 - - + -
875D LEU* 3.4 46.5 + - + +
877D LEU* 3.7 16.4 - - + -
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Residues in contact with ARG 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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120A HIS 3.2 16.4 + - - +
121A GLN 3.0 3.6 + - - +
123A ARG* 1.3 98.2 - - - +
125A GLU* 1.3 60.7 + - - +
126A ILE 3.2 0.2 - - - -
127A GLU* 3.0 24.0 + - - +
128A ILE* 2.8 54.7 + - + +
195A LYS 4.8 10.1 + - - -
246A GLU* 4.0 15.5 + - + +
248A ARG* 3.8 38.0 - - + +
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Residues in contact with GLU 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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121A GLN 2.5 22.9 + - - +
122A LEU* 3.6 7.9 - - - +
124A ARG* 1.3 72.7 - - - +
126A ILE* 1.3 56.5 + - - +
128A ILE* 3.1 8.5 + - - +
129A GLN* 2.9 37.8 + - - +
199A ARG* 3.0 25.1 + - - -
218A ASP* 2.9 25.6 - - - +
219A PHE* 3.3 39.4 - - + -
220A GLY 4.7 0.9 + - - -
248A ARG* 3.7 20.9 + - - +
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Residues in contact with ILE 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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122A LEU* 2.8 32.1 + - + +
123A ARG* 3.5 5.8 - - - +
125A GLU* 1.3 72.1 - - - +
127A GLU* 1.3 53.0 + - - +
129A GLN* 3.4 2.1 + - - +
130A ALA* 2.7 33.1 + - - +
140A LEU* 4.3 19.0 - - + +
143A TYR* 4.1 31.6 - - + -
150A ILE* 5.5 1.6 - - + -
152A LEU* 4.2 19.1 - - + -
219A PHE* 5.0 4.5 - - + -
872D ILE* 3.7 24.7 - - + -
873D LEU 4.6 3.4 - - - +
874D PRO* 6.0 0.7 - - + -
875D LEU* 4.2 26.7 - - + +
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Residues in contact with GLU 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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123A ARG* 3.2 20.7 + - - +
124A ARG* 3.0 28.2 + - - +
126A ILE* 1.3 76.7 - - - +
128A ILE* 1.3 62.5 + - - +
130A ALA* 3.2 12.6 - - + +
131A HIS* 3.0 38.7 + - + +
872D ILE* 5.6 0.4 - - - -
874D PRO* 4.6 20.8 - - + +
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Residues in contact with ILE 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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124A ARG* 2.8 52.2 + - + +
125A GLU* 3.1 12.1 + - - +
127A GLU* 1.3 79.7 - - - +
129A GLN* 1.3 65.3 + - - +
131A HIS* 3.5 15.8 + - - -
132A LEU* 3.7 22.2 - - + +
196A VAL* 3.6 40.3 - - + +
199A ARG* 3.3 30.1 - - - +
248A ARG* 4.6 10.5 - - - +
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Residues in contact with GLN 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 GLU* 2.9 29.6 + - - +
128A ILE* 1.3 73.5 - - - +
130A ALA* 1.3 66.8 + - - +
131A HIS 2.9 1.6 + - - -
132A LEU* 3.0 32.5 + - - +
133A HIS* 5.1 0.5 - - - -
137A ILE* 4.6 4.3 - - - +
138A LEU 4.1 15.4 - - - +
139A ARG* 5.5 1.6 + - - -
140A LEU* 3.6 35.8 + - + +
199A ARG* 3.1 31.7 - - - +
218A ASP* 3.6 14.5 + - - +
219A PHE* 3.7 27.3 - - + -
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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 ILE 2.7 23.6 + - - +
127A GLU* 3.2 15.0 - - + +
128A ILE 3.2 0.2 - - - -
129A GLN* 1.3 73.2 - - - +
131A HIS* 1.3 65.4 + - + +
133A HIS* 3.5 16.3 - - - -
140A LEU* 5.2 1.5 - - - +
872D ILE* 3.7 45.0 - - + +
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Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 3.0 37.5 + - + +
128A ILE* 3.5 8.4 + - - -
129A GLN 3.1 0.4 - - - -
130A ALA* 1.3 82.7 - - + +
132A LEU* 1.3 62.5 - - - +
133A HIS* 3.9 12.8 - - - +
194A LYS* 3.4 40.2 + - + +
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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