Contacts of the helix formed by residues 104 - 121 (chain A) in PDB entry 1H7B
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 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PRO* 3.3 4.5 - - - +
103A LYS* 1.3 84.1 - - - +
105A ILE* 1.3 65.3 + - - +
106A GLY* 3.1 13.7 + - - -
107A VAL* 3.4 18.8 + - - +
108A ALA* 3.2 22.2 + - - +
139A TYR* 3.9 7.6 - - - +
143A THR* 3.7 13.1 + - - -
146A LYS* 5.3 8.1 - - - -
170A ASP* 5.1 3.5 + - - -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 1.3 73.6 + - - +
106A GLY* 1.3 66.7 + - - +
108A ALA* 3.3 0.9 + - - -
109A THR* 3.1 27.0 + - + +
136A LEU* 3.9 29.8 - - + +
139A TYR* 3.5 19.9 + - + +
140A VAL* 3.5 27.4 - - + -
143A THR* 3.1 19.3 + - - +
170A ASP* 3.8 24.5 - - + +
171A VAL* 4.0 18.2 - - + -
174A ALA* 4.3 9.2 - - + -
175A PHE* 4.3 13.7 - - + -
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 3.1 7.1 + - - -
105A ILE* 1.3 84.2 - - - +
107A VAL* 1.3 59.6 + - - +
109A THR* 3.3 3.0 + - - -
110A ALA* 3.3 23.4 + - - +
170A ASP 4.9 1.3 - - - -
174A ALA* 3.8 19.5 - - - -
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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
----------------------------------------------------------
100A GLU 5.8 0.2 - - - +
102A PRO* 3.9 15.5 - - + -
103A LYS* 4.6 2.7 - - + +
104A SER* 3.4 24.7 + - - +
105A ILE 3.1 0.4 - - - -
106A GLY* 1.3 78.4 - - - +
108A ALA* 1.3 59.4 + - - +
109A THR 3.3 0.2 - - - -
110A ALA* 3.7 7.0 - - + +
111A ILE* 2.9 50.9 + - + +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.1 7.7 - - + +
102A PRO* 3.4 31.2 - - + -
104A SER 3.2 11.4 + - - +
105A ILE 3.3 3.3 + - - +
107A VAL* 1.3 80.0 - - - +
109A THR* 1.3 59.0 + - - +
111A ILE* 3.6 3.8 + - - +
112A MET* 3.0 23.4 + - - +
136A LEU* 3.8 25.5 - - + +
139A TYR* 3.9 11.4 - - + -
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.1 20.4 + - + +
106A GLY 3.3 7.3 + - - -
108A ALA* 1.3 74.4 - - - +
110A ALA* 1.3 68.6 + - - +
111A ILE 3.2 0.4 - - - -
112A MET* 3.5 10.9 - - + +
113A ALA* 3.1 18.0 + - - +
136A LEU* 3.9 24.7 - - + -
174A ALA* 3.2 30.8 + - + +
175A PHE* 4.0 23.3 - - + -
177A ALA* 5.7 0.3 - - - +
178A TYR* 3.7 16.8 - - - +
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Residues in contact with ALA 110 (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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106A GLY 3.3 16.2 + - - +
107A VAL* 3.7 9.2 - - + +
108A ALA 3.3 0.2 - - - -
109A THR* 1.3 82.1 + - - +
111A ILE* 1.3 61.5 + - + +
113A ALA* 3.2 16.7 + - - +
114A GLN* 3.2 24.2 + - - +
181A GLU* 4.6 5.5 - - - +
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.9 19.7 - - + -
92A PHE* 4.2 14.8 - - + -
94A LEU* 5.7 0.4 - - + -
99A ILE* 3.6 26.0 - - + -
100A GLU 4.5 3.8 - - - +
102A PRO* 3.9 16.6 - - + -
107A VAL* 2.9 37.9 + - + +
108A ALA* 3.7 5.4 - - - +
110A ALA* 1.3 76.9 - - + +
112A MET* 1.3 63.6 + - - +
114A GLN* 3.2 20.1 + - + +
115A ILE* 3.0 34.2 + - + +
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Residues in contact with MET 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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84A LEU* 3.7 41.5 - - + -
108A ALA 3.0 18.9 + - - +
109A THR* 3.5 8.1 - - + +
110A ALA 3.2 0.4 - - - -
111A ILE* 1.3 75.8 - - - +
113A ALA* 1.3 52.8 + - - +
115A ILE* 3.3 3.9 + - - +
116A THR* 2.7 35.4 + - - -
129A PHE* 3.9 20.9 - - + -
132A VAL* 4.2 7.0 - - + -
136A LEU* 4.0 23.3 - - + -
175A PHE* 4.4 11.4 - - + -
178A TYR* 3.5 42.0 - - + -
197A ILE* 4.4 6.3 - - + -
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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 THR 3.1 12.5 + - - +
110A ALA* 3.3 11.2 - - - +
112A MET* 1.3 73.9 - - - +
114A GLN* 1.3 60.2 + - - +
116A THR* 3.2 5.1 + - - -
117A ALA* 2.9 24.6 + - - +
178A TYR* 3.7 18.8 - - + +
181A GLU* 3.4 39.9 - - + +
182A VAL 5.5 0.2 - - - +
185A LEU* 3.6 11.1 - - + +
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.6 29.2 - - + +
99A ILE* 5.4 3.5 - - - +
110A ALA* 3.3 19.2 + - - +
111A ILE* 3.2 22.7 + - - +
113A ALA* 1.3 77.6 - - + +
115A ILE* 1.3 62.9 + - - +
117A ALA* 3.5 6.3 + - - +
118A GLN* 3.1 28.3 + - - +
181A GLU* 5.2 5.6 - - - +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.0 6.5 - - + -
84A LEU* 3.9 13.7 - - + -
87A MET* 3.3 39.9 - - + -
88A LEU* 5.0 0.7 - - + -
92A PHE* 3.6 37.5 - - + -
94A LEU* 5.2 2.9 - - + -
111A ILE* 3.0 22.0 + - + +
112A MET* 3.5 7.0 - - - +
114A GLN* 1.3 75.2 - - - +
116A THR* 1.3 65.1 + - - +
118A GLN* 3.1 6.4 + - - +
119A VAL* 2.8 33.5 + - + +
129A PHE* 4.0 15.5 - - + -
369A ILE* 4.8 5.8 - - + -
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Residues in contact with THR 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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112A MET 2.7 19.8 + - - -
113A ALA* 3.3 11.0 - - - -
115A ILE* 1.3 75.8 - - - +
117A ALA* 1.3 63.6 + - - +
119A VAL* 4.3 3.3 - - - +
120A ALA* 3.1 26.6 + - - +
127A THR* 4.9 5.9 + - + -
129A PHE* 2.9 15.0 - - + -
178A TYR* 2.8 29.2 + - - +
182A VAL* 4.4 7.4 - - + -
185A LEU* 4.9 2.7 - - + -
193A PRO* 4.4 13.7 - - + -
195A VAL* 4.0 25.8 - - + -
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Residues in contact with ALA 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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113A ALA 2.9 16.4 + - - +
114A GLN* 3.7 7.6 - - - +
115A ILE 3.2 0.2 - - - -
116A THR* 1.3 78.3 - - - +
118A GLN* 1.3 66.0 + - + +
120A ALA* 3.5 4.5 + - - +
121A SER* 3.2 25.6 + - - -
185A LEU* 3.8 31.2 - - + +
186A PHE 4.9 5.8 - - - +
187A SER* 5.0 1.7 - - - -
193A PRO* 5.1 0.2 - - - -
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Residues in contact with GLN 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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94A LEU* 3.6 24.4 - - + +
114A GLN 3.1 18.8 + - - +
115A ILE 3.1 4.0 + - - +
117A ALA* 1.3 78.8 - - + +
119A VAL* 1.3 62.3 + - - +
121A SER* 3.3 7.9 + - - -
122A HIS* 2.6 50.7 + - - -
369A ILE* 4.0 22.4 - - + +
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Residues in contact with VAL 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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80A CYS* 3.9 7.2 - - - -
82A VAL* 4.2 4.7 - - + -
115A ILE* 2.8 31.8 + - + +
116A THR 4.3 0.4 - - - +
118A GLN* 1.3 70.9 - - - +
120A ALA* 1.3 63.7 + - - +
122A HIS* 2.8 14.2 + - - +
123A GLN* 3.3 30.5 + - - +
127A THR* 3.3 33.4 - - + +
369A ILE* 4.3 6.1 - - + -
370A LEU* 3.9 14.8 - - + +
375A ALA* 3.8 28.9 - - + -
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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
----------------------------------------------------------
116A THR* 3.1 19.5 + - + +
117A ALA 3.6 6.1 - - - +
119A VAL* 1.3 77.9 - - - +
121A SER* 1.3 55.6 + - - +
123A GLN* 2.9 23.1 - - - +
125A GLY 5.3 4.1 - - - +
127A THR* 4.1 10.4 + - - +
187A SER* 3.6 24.4 + - - +
193A PRO* 3.8 20.6 - - + -
194A PHE 5.6 0.4 - - - +
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Residues in contact with SER 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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76A PHE* 4.3 9.8 - - - -
117A ALA 3.2 12.6 + - - -
118A GLN* 3.3 14.1 + - - -
119A VAL 3.0 1.0 + - - -
120A ALA* 1.3 76.2 - - - +
122A HIS* 1.3 74.4 + - - +
123A GLN 3.6 1.6 - - - -
187A SER* 3.9 4.3 - - - -
188A SER* 3.4 42.9 + - - +
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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
------------------------------------------------------------
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