Contacts of the helix formed by residues 113 - 124 (chain A) in PDB entry 4M83
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 SER 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.7 30.2 - - - +
13A SER* 4.7 9.7 + - - -
14A ILE* 5.3 3.6 - - - -
59A TYR* 5.7 1.0 + - - -
95A LEU* 5.4 1.0 - - - +
109A HIS* 4.0 1.8 + - - -
110A ASP 3.2 12.2 + - - -
111A ILE 3.3 0.4 - - - -
112A THR* 1.3 77.6 + - - +
114A TYR* 1.3 61.5 + - - +
115A PRO* 3.7 10.5 - - - +
116A ALA* 3.4 30.4 + - - +
117A ARG* 2.9 16.3 + - - +
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Residues in contact with TYR 114 (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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81A VAL* 4.9 3.7 + - - +
84A PHE* 3.6 25.3 - - + +
85A LEU* 3.8 22.0 - - + -
88A ALA* 3.6 12.8 - - + +
111A ILE 4.5 4.3 - - - -
112A THR 3.2 5.7 + - - -
113A SER* 1.3 70.0 - - - +
115A PRO* 1.4 74.8 - - + +
117A ARG* 3.1 37.3 + - - +
118A VAL* 3.1 15.7 + - - +
161A TYR* 4.8 4.2 + - - -
165A PHE* 3.5 34.7 - + - -
168A TRP* 3.9 7.2 - + + -
181A PHE* 3.9 16.8 - + + -
182A ALA* 4.1 17.6 - - + +
1400A ERY 3.9 31.6 + - + +
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Residues in contact with PRO 115 (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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59A TYR* 6.1 0.4 - - + -
88A ALA* 3.7 32.3 - - + +
91A ALA* 3.9 15.3 - - + -
92A LEU* 4.0 22.0 - - + +
95A LEU* 3.9 21.8 - - + -
113A SER* 3.5 11.0 - - - +
114A TYR* 1.4 93.8 - - + +
116A ALA* 1.3 52.9 + - - +
118A VAL* 3.1 5.0 + - + +
119A LEU* 2.7 41.8 + - + +
168A TRP* 5.1 0.7 - - + -
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Residues in contact with ALA 116 (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 PHE* 3.6 28.2 - - + -
107A VAL* 3.8 7.1 - - + +
109A HIS* 3.3 36.6 - - + -
113A SER* 3.4 15.5 + - - +
114A TYR 3.2 0.8 - - - -
115A PRO* 1.3 78.3 - - - +
117A ARG* 1.3 57.2 + - - +
119A LEU* 4.1 1.5 - - - +
120A ALA* 2.9 32.6 + - - +
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Residues in contact with ARG 117 (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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109A HIS* 3.8 27.5 - - + +
111A ILE* 2.8 41.6 + - - +
113A SER 2.9 27.5 + - - +
114A TYR* 3.1 17.4 + - - +
116A ALA* 1.3 79.0 - - - +
118A VAL* 1.3 64.0 + - - +
120A ALA* 3.8 4.5 - - - +
121A ARG* 2.9 39.8 + - - +
127A ALA* 5.5 2.7 - - - -
129A SER* 5.4 0.8 + - - -
181A PHE* 3.0 54.4 + - + -
182A ALA* 2.9 26.2 + - - +
185A PRO* 6.2 4.0 - - - +
1400A ERY 4.7 1.4 - - - +
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Residues in contact with VAL 118 (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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92A LEU* 3.8 17.7 - - + -
114A TYR 3.1 11.6 + - - +
115A PRO 3.1 6.2 + - - +
117A ARG* 1.3 77.8 - - - +
119A LEU* 1.3 59.6 + - - +
121A ARG* 3.2 12.9 + - - +
122A ARG* 3.0 30.4 + - + +
168A TRP* 3.8 26.5 - - + -
169A LEU* 4.7 1.3 - - + -
172A ASN* 3.5 36.1 - - + +
174A ILE* 4.0 10.0 - - + +
181A PHE* 3.8 15.0 - - + -
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Residues in contact with LEU 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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12A PHE* 4.1 11.2 - - + -
92A LEU* 3.6 22.4 - - + -
95A LEU* 3.7 30.7 - - + -
96A ALA* 3.7 26.2 - - + +
115A PRO* 2.7 25.2 + - + +
116A ALA* 4.1 3.1 - - - +
118A VAL* 1.3 71.9 - - - +
120A ALA* 1.3 65.6 + - - +
122A ARG* 3.0 18.0 + - - +
123A TRP* 2.9 67.4 + - + +
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Residues in contact with ALA 120 (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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107A VAL* 3.8 21.5 - - + -
116A ALA 2.9 19.8 + - - +
117A ARG 3.8 3.8 - - - +
119A LEU* 1.3 75.3 - - - +
121A ARG* 1.3 62.9 + - + +
123A TRP* 3.1 3.4 + - - -
124A GLY 3.1 17.3 + - - -
125A VAL* 3.2 25.3 + - - +
127A ALA* 3.6 28.9 - - + -
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Residues in contact with ARG 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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117A ARG* 2.9 38.1 + - - +
118A VAL* 3.2 5.3 + - - +
119A LEU 3.2 0.6 - - - -
120A ALA* 1.3 77.7 - - + +
122A ARG* 1.3 62.5 + - - +
123A TRP 3.3 0.5 + - - -
124A GLY* 3.3 11.9 + - - -
125A VAL 5.3 0.4 - - - -
174A ILE* 3.6 30.4 - - + +
176A GLU* 2.1 43.8 + - - +
181A PHE* 3.8 14.3 + - - +
186A PRO* 5.2 14.8 - - - +
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Residues in contact with ARG 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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92A LEU* 3.9 16.6 - - - +
96A ALA* 3.2 31.7 - - - +
118A VAL* 3.0 16.9 + - - +
119A LEU* 3.0 24.4 + - - +
121A ARG* 1.3 77.1 - - - +
123A TRP* 1.3 70.8 + - + +
124A GLY 3.6 0.3 + - - -
172A ASN* 3.0 26.3 + - - -
335B ASP* 5.2 12.3 + - - +
345B LYS* 5.6 6.8 - - - +
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Residues in contact with TRP 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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12A PHE* 4.1 5.6 - + - -
95A LEU 4.9 0.9 - - - -
96A ALA* 5.1 3.2 + - - +
99A TYR* 3.4 44.7 + + + +
100A ALA* 6.2 0.4 - - - +
103A ILE* 3.8 31.2 - - + +
104A PRO* 3.3 24.5 - - + -
107A VAL* 3.5 28.3 - - + -
119A LEU* 2.9 54.6 + - + +
120A ALA 3.7 4.3 - - - +
121A ARG 3.1 0.4 - - - -
122A ARG* 1.3 89.7 - - + +
124A GLY* 1.3 62.5 + - - +
125A VAL* 3.4 22.3 - - + +
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Residues in contact with GLY 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 ALA 3.1 4.1 + - - -
121A ARG* 3.3 12.0 + - - -
122A ARG 3.4 1.0 + - - -
123A TRP* 1.3 78.8 - - - +
125A VAL* 1.3 60.1 + - - +
126A PRO* 4.7 0.9 - - - +
350B GLU* 5.4 12.3 - - - +
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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