Contacts of the helix formed by residues 101 - 114 (chain A) in PDB entry 1IVV
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 LEU 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.7 22.0 - - + -
39A ILE 3.7 11.0 - - - +
40A ALA* 3.7 35.7 - - + +
65A HIS* 3.5 31.0 - - + -
67A VAL* 5.3 0.2 - - + -
99A PRO 4.4 3.6 - - - +
100A VAL* 1.3 74.8 - - - +
102A GLU* 1.3 66.1 + - - +
103A GLU* 3.9 21.8 - - + +
104A GLU* 3.0 36.3 + - + +
105A PHE* 3.3 13.4 + - - -
151A ARG* 4.9 0.7 - - - +
306A GLN* 5.8 0.9 - - - +
331A ALA* 4.8 8.7 - - + -
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Residues in contact with GLU 102 (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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100A VAL 4.1 1.2 + - - -
101A LEU* 1.3 72.7 - - - +
103A GLU* 1.3 60.2 + - - +
105A PHE* 3.1 22.7 + - + +
106A GLU* 2.9 40.9 + - + +
306A GLN* 4.2 18.9 + - - +
307A TYR* 3.8 34.2 + - + +
336A ARG* 5.3 7.8 + - - -
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Residues in contact with GLU 103 (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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38A ARG* 3.2 36.8 + - - +
67A VAL* 3.9 15.2 - - - +
101A LEU* 3.9 22.5 - - + +
102A GLU* 1.3 79.8 - - - +
104A GLU* 1.3 68.9 + - + +
106A GLU* 3.3 25.7 + - - +
107A VAL* 3.3 13.9 + - - +
331A ALA* 4.5 8.0 - - + +
332A PHE* 4.2 8.7 - - - -
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Residues in contact with GLU 104 (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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65A HIS* 3.7 11.6 + - - -
100A VAL* 3.6 9.3 - - + +
101A LEU* 3.0 41.7 + - + +
103A GLU* 1.3 79.1 - - + +
105A PHE* 1.3 67.6 + - - +
107A VAL* 3.2 25.1 - - - +
108A VAL* 3.7 7.8 - - - +
151A ARG* 2.7 40.2 + - - -
153A LEU* 3.8 3.6 - - - +
181A VAL* 3.5 36.0 - - + +
182A VAL* 4.7 1.9 - - - +
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Residues in contact with PHE 105 (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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100A VAL* 3.3 40.6 - - + -
101A LEU 3.3 13.0 + - - -
102A GLU* 3.1 19.2 + - + +
104A GLU* 1.3 81.0 - - - +
106A GLU* 1.3 64.3 + - + +
107A VAL 3.3 0.2 + - - -
108A VAL* 3.4 9.4 + - - +
109A GLU* 4.7 0.9 + - - +
136A PRO* 3.3 54.0 - - + +
137A LEU* 5.0 0.7 - - - -
153A LEU* 3.6 19.5 - - + -
302A TYR* 3.7 32.5 - + + -
307A TYR* 3.5 22.4 - + - -
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Residues in contact with GLU 106 (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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102A GLU* 2.9 37.8 - - + +
103A GLU* 3.4 17.0 - - - +
104A GLU 3.2 0.2 - - - -
105A PHE* 1.3 77.5 - - + +
107A VAL* 1.3 61.2 + - - +
108A VAL 3.3 0.9 + - - -
109A GLU* 3.9 9.7 + - - +
110A GLN* 3.4 26.4 + - - +
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Residues in contact with VAL 107 (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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103A GLU 3.3 7.6 + - - +
104A GLU* 3.2 20.2 - - - +
106A GLU* 1.3 77.1 - - - +
108A VAL* 1.3 65.7 + - - +
109A GLU 3.5 0.2 - - - -
110A GLN* 3.3 21.6 + - + +
111A LEU* 3.0 47.9 + - + +
181A VAL* 4.0 24.9 - - + +
184A LYS* 4.5 24.0 - - + +
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Residues in contact with VAL 108 (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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104A GLU 3.7 3.8 - - - +
105A PHE 3.7 7.4 - - - +
106A GLU 3.3 1.6 - - - -
107A VAL* 1.3 77.8 - - - +
109A GLU* 1.3 64.6 + - - +
111A LEU* 3.4 1.6 + - - +
112A LEU* 3.1 28.8 + - + +
134A VAL* 3.9 22.0 - - + -
136A PRO* 3.6 15.9 - - + -
153A LEU* 3.6 38.6 - - + -
155A GLY* 4.6 9.0 - - - +
179A VAL* 3.9 27.3 - - + +
181A VAL* 4.3 7.0 - - + -
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Residues in contact with GLU 109 (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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105A PHE 4.7 0.8 + - - +
106A GLU 3.9 7.6 + - - +
107A VAL 3.5 0.2 - - - -
108A VAL* 1.3 78.3 - - - +
110A GLN* 1.3 63.5 + - + +
112A LEU* 3.4 2.3 + - - +
113A ALA* 3.0 25.3 + - + +
118A TRP* 5.7 0.2 + - - -
129A VAL 6.0 0.2 - - - +
132A VAL 3.4 13.6 - - - +
133A ARG* 2.9 43.1 + - - -
134A VAL* 3.0 45.1 + - + +
359B TRP* 4.7 3.3 + - - -
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Residues in contact with GLN 110 (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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106A GLU* 3.4 32.4 + - - +
107A VAL* 3.4 22.6 - - + +
109A GLU* 1.3 76.5 - - + +
111A LEU* 1.3 65.5 + - + +
113A ALA* 3.2 19.7 + - - +
114A THR* 3.8 9.9 + - - +
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Residues in contact with LEU 111 (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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107A VAL* 3.0 32.8 + - + +
108A VAL 3.9 2.9 - - - +
110A GLN* 1.3 81.3 - - + +
112A LEU* 1.3 64.0 + - - +
114A THR* 3.1 22.9 + - - +
115A ASP* 3.4 8.3 + - - +
179A VAL* 3.4 31.0 - - + -
184A LYS* 3.5 47.1 - - + +
185A GLU* 4.2 2.2 - - - +
186A VAL* 4.2 13.3 - - + +
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Residues in contact with LEU 112 (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 VAL* 3.1 35.0 + - + +
109A GLU* 3.8 3.6 - - - +
111A LEU* 1.3 79.8 - - - +
113A ALA* 1.3 57.6 + - - +
115A ASP* 2.9 19.9 + - - +
118A TRP* 3.2 66.0 - - + +
134A VAL* 4.0 14.6 - - + -
155A GLY* 5.1 0.9 - - - -
177A ALA* 3.3 32.3 - - + -
179A VAL* 4.2 7.2 - - + -
186A VAL* 3.9 24.2 - - + -
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Residues in contact with ALA 113 (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 GLU* 3.0 15.7 + - + +
110A GLN* 3.3 14.1 - - - +
111A LEU 3.1 0.4 - - - -
112A LEU* 1.3 76.1 - - - +
114A THR* 1.3 62.0 + - + +
118A TRP* 4.5 0.7 - - - +
119A LEU* 3.3 24.7 - - - +
129A VAL* 3.9 27.0 - - + +
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Residues in contact with THR 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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110A GLN 4.1 8.3 + - - +
111A LEU* 3.1 15.2 + - - +
112A LEU 3.1 0.6 - - - -
113A ALA* 1.3 81.5 - - + +
115A ASP* 1.3 60.5 + - - +
116A GLU* 3.8 5.9 + - - +
119A LEU* 4.2 7.1 - - - +
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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