Contacts of the helix formed by residues 103 - 115 (chain A) in PDB entry 1X7H
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 ALA 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU 3.4 5.1 + - - +
102A LEU* 1.3 78.1 - - - +
104A ASP* 1.3 65.7 + - - +
105A GLU* 4.2 5.6 - - + +
106A LEU* 3.0 30.3 + - + +
107A TRP* 3.2 10.0 + - - +
123B LYS* 4.5 2.0 - - - +
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Residues in contact with ASP 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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102A LEU 3.5 3.2 + - - -
103A ALA* 1.3 71.8 - - - +
105A GLU* 1.3 58.6 + - - +
107A TRP* 3.3 5.4 + - - +
108A LEU* 3.0 37.5 + - - +
67B VAL* 3.9 13.8 - - + +
116B THR* 5.1 0.5 - - - +
119B PHE* 4.0 14.1 - - - -
120B ARG* 2.9 55.4 + - - +
123B LYS* 4.0 10.0 + - - +
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Residues in contact with GLU 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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103A ALA* 3.1 6.1 - - + +
104A ASP* 1.3 77.5 + - - +
106A LEU* 1.3 59.7 + - - +
108A LEU* 3.2 24.6 + - + +
109A ASP* 2.8 40.9 + - - +
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Residues in contact with LEU 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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93A ARG* 3.7 29.8 - - - +
95A GLY* 4.7 3.8 - - - -
96A GLY 3.8 17.7 - - - +
102A LEU* 3.6 30.1 - - + -
103A ALA* 3.0 23.3 + - + +
105A GLU* 1.3 78.3 - - - +
107A TRP* 1.3 64.2 + - - +
109A ASP* 3.2 2.7 + - - -
110A VAL* 3.0 43.4 + - + +
156A PRO* 5.3 0.9 - - + -
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Residues in contact with TRP 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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102A LEU* 3.8 10.9 - - + +
103A ALA 3.2 3.6 + - - +
104A ASP* 3.3 8.0 + - - +
106A LEU* 1.3 79.8 - - - +
108A LEU* 1.3 68.7 + - + +
110A VAL* 3.5 1.6 + - - +
111A VAL* 3.1 44.0 + - + +
155A ALA* 4.1 0.4 - - + -
156A PRO* 3.5 39.7 - - + -
159A ALA* 3.6 20.4 - - + -
115B LEU* 3.4 28.7 - - + -
116B THR* 3.2 40.7 + - + +
119B PHE* 3.5 53.4 - + + -
167B PHE* 3.6 28.0 - + - -
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Residues in contact with LEU 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 ASP* 3.0 32.9 + - - +
105A GLU* 3.6 28.5 - - + +
106A LEU 3.2 0.2 - - - -
107A TRP* 1.3 80.5 - - + +
109A ASP* 1.3 56.1 + - - +
111A VAL* 3.9 3.5 - - + +
112A GLU* 2.9 32.9 + - - +
112B GLU* 5.9 2.7 - - + -
116B THR* 3.9 23.8 - - + +
120B ARG* 3.7 22.0 - - - +
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Residues in contact with ASP 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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65A ARG* 2.6 41.1 + - - -
93A ARG* 2.5 35.4 + - - +
105A GLU* 2.8 28.4 + - - +
106A LEU* 3.9 4.7 - - - +
108A LEU* 1.3 72.3 - - - +
110A VAL* 1.3 60.7 + - - +
112A GLU* 4.0 3.5 - - - +
113A THR* 2.8 38.1 + - - -
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Residues in contact with VAL 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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93A ARG* 3.5 31.9 - - - +
94A PRO 4.0 5.8 - - - +
95A GLY* 4.0 6.7 - - - -
106A LEU* 3.0 29.1 + - + +
107A TRP 4.0 2.7 - - - +
109A ASP* 1.3 76.8 - - - +
111A VAL* 1.3 58.1 + - - +
113A THR* 4.7 0.2 - - - -
114A ASN* 2.9 41.2 + - - +
156A PRO* 3.6 27.4 - - + +
157A TYR* 3.9 6.3 - - + +
160A SER* 3.1 18.2 + - - +
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Residues in contact with VAL 111 (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 TRP* 3.1 49.1 + - + +
108A LEU* 3.9 4.5 - - - +
110A VAL* 1.3 75.6 - - + +
112A GLU* 1.3 59.8 + - - +
115A LEU* 2.9 38.1 + - + +
116A THR* 3.0 14.1 + - - +
156A PRO 4.8 4.0 - - - +
160A SER* 3.4 16.2 - - - +
111B VAL* 4.0 27.4 - - + -
115B LEU* 4.5 6.5 - - + -
116B THR* 5.0 3.6 - - - +
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Residues in contact with GLU 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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64A VAL 4.5 1.9 - - - +
65A ARG* 3.6 30.3 - - + +
108A LEU 2.9 18.5 + - - +
109A ASP* 4.0 5.4 - - - +
111A VAL* 1.3 77.1 - - - +
113A THR* 1.3 58.1 + - - +
116A THR* 3.4 10.9 + - - +
117A GLY* 2.9 25.6 + - - -
120A ARG* 2.9 30.7 + - - +
108B LEU* 4.2 16.3 - - - +
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Residues in contact with THR 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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64A VAL* 3.8 22.8 - - + +
65A ARG* 3.3 25.4 + - - -
91A ALA* 3.9 12.6 - - + +
92A GLY 5.0 0.9 - - - +
93A ARG* 3.8 19.5 - - + +
109A ASP* 2.8 27.7 + - - -
110A VAL 4.1 0.4 - - - -
112A GLU* 1.3 80.0 - - - +
114A ASN* 1.3 75.0 + - - +
117A GLY* 3.6 14.0 - - - -
301A NDP 4.0 16.1 + - + +
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Residues in contact with ASN 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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91A ALA* 3.8 16.2 - - + +
93A ARG* 2.9 50.4 + - - +
110A VAL* 2.9 33.5 + - - +
113A THR* 1.3 78.6 - - - +
115A LEU* 1.3 58.0 + - - +
117A GLY 4.5 0.2 - - - -
118A VAL* 3.9 7.8 - - - +
157A TYR* 3.9 15.2 - - - -
160A SER* 3.6 15.7 - - - -
161A LYS* 4.1 13.4 + - + +
164A VAL* 3.2 21.1 - - - +
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Residues in contact with LEU 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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111A VAL* 2.9 28.6 + - + +
114A ASN* 1.3 73.4 - - - +
116A THR* 1.3 64.3 + - - +
117A GLY 3.1 1.3 - - - -
118A VAL* 2.7 33.1 - - + +
119A PHE 3.3 2.4 + - - -
160A SER* 3.7 20.6 - - - +
163A GLY* 3.9 28.3 - - - +
164A VAL* 4.1 2.9 - - - +
167A PHE* 4.7 0.9 - - + -
107B TRP* 3.5 30.0 - - + -
111B VAL* 4.5 10.5 - - + -
115B LEU* 4.2 25.1 - - + -
159B ALA* 4.1 11.9 - - + +
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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
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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