Contacts of the helix formed by residues 112 - 130 (chain A) in PDB entry 3IHL
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 GLN 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A THR* 4.1 19.7 - - + +
111A VAL* 1.3 81.0 - - - +
113A VAL* 1.3 64.5 + - - +
114A VAL 3.3 22.0 + - - +
115A PRO* 4.4 3.5 - - + +
116A HIS* 3.0 35.0 + - + +
117A ILE* 3.5 3.4 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.9 29.6 - - + +
112A GLN* 1.3 70.8 - - - +
114A VAL* 1.3 67.3 + - + +
117A ILE* 3.0 42.1 + - + +
118A THR* 3.1 15.8 + - + +
158A PRO* 4.4 18.2 - - + -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLN* 3.3 20.6 - - - +
113A VAL* 1.3 84.1 - - + +
115A PRO* 1.3 68.5 - - + +
116A HIS 3.7 0.4 - - - -
118A THR* 3.7 7.0 - - + +
161A GLU* 3.9 24.7 - - + +
165A GLN* 3.4 27.4 - - - +
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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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112A GLN* 4.4 5.4 - - + +
114A VAL* 1.3 87.1 - - + +
116A HIS* 1.3 82.5 + - + +
117A ILE 3.6 0.7 - - - -
118A THR* 3.3 11.2 - - - +
119A ASP* 2.7 55.5 + - - +
165A GLN* 5.4 3.8 - - - +
233B PHE* 6.3 4.0 - - + -
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Residues in contact with HIS 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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97A VAL* 3.8 11.1 - - + +
106A TYR* 3.8 35.9 + + - +
109A LYS* 5.8 3.0 - - + +
110A THR 3.5 23.9 + - - -
111A VAL* 3.6 21.2 - - + +
112A GLN* 3.0 31.4 + - + +
115A PRO* 1.3 96.6 - - + +
117A ILE* 1.3 62.9 + - - +
119A ASP* 3.8 8.8 - - - +
120A ALA* 3.2 21.5 + - - +
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.1 20.9 - - + +
94A TYR* 4.1 43.5 - - + +
97A VAL* 3.7 33.0 - - + -
98A ILE* 6.5 0.2 - - + -
112A GLN 4.4 1.6 - - - +
113A VAL* 3.0 37.7 + - + +
116A HIS* 1.3 74.2 - - - +
118A THR* 1.3 60.2 + - - +
120A ALA* 2.9 6.1 + - - +
121A VAL* 2.8 34.3 + - + +
158A PRO* 4.5 9.9 - - + -
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Residues in contact with THR 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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113A VAL* 3.1 16.4 + - + +
114A VAL* 3.7 12.3 - - + +
115A PRO* 3.1 24.6 + - - +
117A ILE* 1.3 80.7 - - + +
119A ASP* 1.3 58.7 + - - +
121A VAL* 3.5 3.1 + - - +
122A GLN* 3.0 33.5 + - - +
158A PRO 3.6 23.1 - - - +
161A GLU* 4.0 21.5 - - + -
162A ALA* 3.9 16.7 - - - +
165A GLN* 4.1 9.4 + - - -
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PRO* 2.7 45.5 + - - +
116A HIS* 3.8 10.6 - - - +
118A THR* 1.3 70.7 + - - +
120A ALA* 1.3 61.7 + - - +
122A GLN* 3.2 14.5 + - - +
123A GLU* 2.8 48.8 + - - +
165A GLN* 4.9 3.1 - - - +
169A LYS* 5.9 1.6 + - - -
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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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93A ILE* 3.7 20.0 - - + +
96A HIS* 4.5 10.3 - - + +
97A VAL* 3.8 17.3 - - + -
116A HIS 3.2 11.7 + - - +
117A ILE 2.9 9.2 + - - +
119A ASP* 1.3 75.2 - - - +
121A VAL* 1.3 61.2 + - - +
123A GLU* 3.6 10.7 + - - +
124A TRP* 2.8 31.9 + - - +
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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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39A ILE* 5.0 2.9 - - + -
88A ILE* 5.7 3.1 - - + -
93A ILE* 3.9 17.7 - - + -
117A ILE* 2.8 25.9 + - + +
118A THR* 3.8 2.7 - - - +
119A ASP 3.3 0.2 - - - -
120A ALA* 1.3 76.6 - - - +
122A GLN* 1.3 58.2 + - + +
124A TRP* 3.2 8.4 + - + +
125A VAL* 3.0 38.6 + - + +
158A PRO 5.0 2.0 - - - +
159A PHE* 3.9 36.1 - - + -
162A ALA* 3.7 26.9 - - + -
163A PHE* 4.8 9.4 - - + -
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Residues in contact with GLN 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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118A THR 3.0 24.6 + - - +
119A ASP* 3.2 12.9 + - - +
121A VAL* 1.3 76.8 - - + +
123A GLU* 1.3 62.4 + - - +
125A VAL* 3.5 5.9 + - - +
126A MET* 3.2 35.9 + - + +
162A ALA* 3.5 30.4 + - + +
163A PHE* 6.1 1.8 - - + -
165A GLN* 3.7 23.8 + - - +
166A PHE* 3.5 30.9 + - + +
169A LYS* 3.3 30.9 - - - +
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Residues in contact with GLU 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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119A ASP* 2.8 40.8 + - - +
120A ALA* 3.6 9.3 + - - +
122A GLN* 1.3 76.6 - - + +
124A TRP* 1.3 62.7 + - - +
126A MET* 3.6 18.7 + - + +
127A ASN* 2.9 37.1 + - - +
169A LYS* 5.4 3.6 - - - +
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Residues in contact with TRP 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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37A ILE* 3.4 37.9 - - + -
39A ILE* 4.8 0.9 - - + -
86A ASN* 3.8 9.6 - - - +
87A ASN 3.8 15.3 - - - -
88A ILE* 3.2 65.1 - - + +
93A ILE* 4.7 6.5 - - + -
120A ALA 2.8 18.8 + - - +
121A VAL* 3.6 6.3 - - + +
123A GLU* 1.3 75.3 - - - +
125A VAL* 1.3 77.9 + - + +
127A ASN* 3.5 5.4 + - + +
128A GLN* 3.1 49.4 + - + +
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Residues in contact with VAL 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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3A TYR* 3.6 24.9 - - + -
37A ILE* 3.7 18.1 - - + +
39A ILE* 5.1 1.8 - - + -
121A VAL* 3.0 24.7 + - + +
122A GLN* 3.9 7.2 - - - +
124A TRP* 1.3 89.6 - - + +
126A MET* 1.3 59.1 + - - +
129A ALA* 2.9 28.8 + - - +
145A ILE* 3.8 17.9 - - + -
163A PHE* 4.0 26.5 - - + -
166A PHE* 4.6 8.7 - - + -
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Residues in contact with MET 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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3A TYR* 3.8 18.8 + - - +
122A GLN* 3.2 22.5 + - + +
123A GLU* 3.7 22.9 - - + +
125A VAL* 1.3 76.0 - - - +
127A ASN* 1.3 64.0 + - - +
129A ALA* 4.0 2.1 - - - +
130A LYS* 3.5 40.0 + - - +
166A PHE* 3.6 26.5 - - + -
169A LYS* 3.5 30.5 - - - +
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Residues in contact with ASN 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 GLU* 2.9 30.6 + - - +
124A TRP* 4.0 4.9 - - + +
125A VAL 3.3 0.4 - - - -
126A MET* 1.3 78.3 - - - +
128A GLN* 1.3 65.7 + - + +
130A LYS* 3.5 23.7 + - - +
131A VAL* 3.5 14.5 - - - +
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Residues in contact with GLN 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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35A THR* 4.8 5.1 + - - -
37A ILE* 3.7 21.1 - - + -
86A ASN* 3.4 34.8 + - - +
124A TRP* 3.1 49.2 + - + +
127A ASN* 1.3 76.0 - - + +
129A ALA* 1.3 66.0 + - - +
130A LYS 3.1 0.2 - - - -
131A VAL* 3.1 35.3 + - - +
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Residues in contact with ALA 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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1A MET* 3.2 40.0 - - + +
3A TYR* 3.8 7.4 - - + -
35A THR* 3.8 11.6 - - - +
37A ILE* 4.2 1.0 - - - +
125A VAL 2.9 18.2 + - - +
126A MET 4.0 4.7 - - - +
128A GLN* 1.3 76.7 - - - +
130A LYS* 1.3 59.6 + - - +
140A PRO* 3.3 16.5 - - - +
143A CYS* 3.8 21.5 - - + -
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Residues in contact with LYS 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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1A MET* 4.1 11.0 - - + +
3A TYR* 5.6 1.6 + - - -
126A MET* 3.5 31.0 + - - +
127A ASN* 3.8 17.7 + - - +
128A GLN 3.1 1.2 - - - -
129A ALA* 1.3 76.3 - - - +
131A VAL* 1.3 62.4 + - + +
132A PRO* 3.4 5.9 - - - +
139A GLU* 3.8 34.2 + - + +
140A PRO* 3.4 11.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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