Contacts of the helix formed by residues 98 - 112 (chain A) in PDB entry 2X7X
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 GLU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ASN* 3.1 25.4 + - - +
96A ALA* 3.9 7.6 - - - +
97A ASN* 1.3 93.8 + - - +
99A ALA* 1.3 65.7 + - - +
100A ALA 3.6 0.4 - - - -
101A PRO* 3.7 17.9 - - + +
102A MET* 3.4 22.2 + - - +
163A LEU* 3.8 24.7 - - + +
165A GLY* 3.4 34.0 + - - +
166A SER* 4.2 0.9 - - - +
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Residues in contact with ALA 99 (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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96A ALA* 5.1 0.4 - - - -
98A GLU* 1.3 71.5 - - - +
100A ALA* 1.3 60.9 + - - +
102A MET 4.1 0.3 - - - -
103A THR* 2.7 33.7 + - - -
122A LYS 3.7 13.6 + - - +
123A ILE* 4.1 3.7 - - - +
124A LEU* 3.7 22.7 - - + -
165A GLY 2.9 14.8 + - - +
166A SER* 4.5 1.2 - - - +
167A THR* 3.6 29.6 - - + -
170A MET* 5.0 6.1 - - + -
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Residues in contact with ALA 100 (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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99A ALA* 1.3 78.9 - - - +
101A PRO* 1.4 70.8 - - + +
102A MET 3.2 1.0 + - - -
103A THR* 3.2 13.4 + - - -
104A PRO* 3.3 10.7 - - - +
124A LEU* 3.8 20.6 - - + +
165A GLY 4.7 0.8 + - - -
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Residues in contact with PRO 101 (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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74A ASN* 3.7 37.5 - - + +
98A GLU* 3.7 20.9 - - + +
100A ALA* 1.4 94.4 - - + +
102A MET* 1.3 62.8 + - - +
104A PRO* 3.6 15.7 - - + +
105A ILE* 4.0 10.0 - - - +
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Residues in contact with MET 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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74A ASN* 3.0 58.8 - - + +
77A GLN* 3.5 35.4 - - - +
78A ALA* 4.3 6.7 - - - -
94A ILE* 4.2 18.4 - - + -
96A ALA* 4.0 13.9 - - + -
97A ASN* 4.3 2.5 - - + -
98A GLU 3.4 15.7 + - - +
99A ALA 3.6 1.6 + - - +
100A ALA 3.2 1.2 - - - -
101A PRO* 1.3 81.9 - - - +
103A THR* 1.3 65.2 + - - +
104A PRO 3.5 0.2 - - - -
105A ILE* 3.2 16.6 + - + -
106A VAL* 3.0 23.0 + - + +
123A ILE* 4.4 2.7 - - + -
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Residues in contact with THR 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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99A ALA 2.7 21.6 + - - -
100A ALA* 3.2 6.0 + - - -
102A MET* 1.3 76.0 - - - +
104A PRO* 1.3 72.9 - - + +
106A VAL* 3.1 3.8 + - - +
107A GLU* 3.0 32.3 + - - +
123A ILE* 3.5 10.0 - - + +
124A LEU* 3.0 30.5 + - + +
125A SER* 3.8 27.4 - - - +
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Residues in contact with PRO 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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100A ALA 3.3 13.9 - - - +
101A PRO* 3.6 12.3 - - + +
103A THR* 1.3 91.8 - - + +
105A ILE* 1.3 67.4 + - + +
107A GLU* 3.2 15.8 + - + +
108A GLU* 3.0 36.5 + - - +
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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
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78A ALA* 4.0 28.7 - - + +
81A VAL* 3.7 42.0 - - + +
82A HIS* 4.4 18.6 - - + +
85A MET* 5.0 0.5 - - - +
101A PRO 4.0 15.3 - - - +
102A MET* 3.2 20.5 + - + +
104A PRO* 1.3 89.6 - - + +
106A VAL* 1.3 61.9 + - + +
108A GLU* 3.6 15.5 - - - +
109A ALA 3.5 13.9 + - - -
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Residues in contact with VAL 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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81A VAL* 5.5 1.6 - - + -
92A LEU* 5.6 1.8 - - + -
94A ILE* 3.9 36.1 - - + -
102A MET* 3.0 19.6 + - + +
103A THR 3.1 2.7 + - - +
105A ILE* 1.3 76.0 - - + +
107A GLU* 1.3 65.1 + - - +
109A ALA* 3.2 8.2 + - - +
110A TYR* 3.0 19.6 + - - +
116A VAL* 3.8 25.4 - - + -
118A LEU* 4.3 3.8 - - + -
123A ILE* 3.8 35.7 - - + -
127A LYS 3.9 9.6 - - - +
128A TYR* 4.8 0.7 - - + -
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Residues in contact with GLU 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 THR* 3.0 20.9 + - - +
104A PRO* 3.2 18.9 + - - +
106A VAL* 1.3 73.8 - - - +
108A GLU* 1.3 54.7 + - - +
110A TYR* 3.0 8.3 + - - +
111A GLN* 2.8 40.0 + - - +
123A ILE* 5.4 0.9 - - + -
125A SER* 2.9 29.9 + - - +
127A LYS* 3.7 38.2 + - + +
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Residues in contact with GLU 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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82A HIS* 3.4 31.1 + - - -
85A MET* 4.0 13.6 - - + +
104A PRO* 3.0 21.9 + - - +
105A ILE* 3.6 19.3 - - - +
107A GLU* 1.3 75.1 - - - +
109A ALA* 1.3 64.3 - - - +
110A TYR 3.1 0.3 + - - -
111A GLN* 3.4 20.5 - - - +
112A LYS* 2.8 29.0 + - + +
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Residues in contact with ALA 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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81A VAL* 4.5 9.2 - - + -
85A MET* 4.0 26.8 - - + -
92A LEU* 4.8 8.3 - - + -
105A ILE 3.5 7.2 + - - +
106A VAL* 3.2 10.8 + - - +
108A GLU* 1.3 78.5 - - - +
110A TYR* 1.3 58.3 + - - +
112A LYS* 3.7 4.5 + - - +
113A GLY 3.7 2.1 + - - -
114A ILE* 3.1 36.6 + - + +
116A VAL* 3.9 15.5 - - + -
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Residues in contact with TYR 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 VAL 3.0 9.0 + - - +
107A GLU* 3.0 9.4 + - - +
109A ALA* 1.3 75.1 - - - +
111A GLN* 1.3 61.3 + - - +
113A GLY* 3.0 20.8 + - - -
114A ILE 4.0 9.6 - - - -
115A PRO* 5.6 0.4 - - + -
116A VAL* 4.3 4.2 - - + +
126A ASP 4.9 2.0 + - - -
127A LYS* 3.5 46.2 - - + +
128A TYR* 3.5 37.1 + - - -
129A THR* 3.8 16.7 - - + +
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Residues in contact with GLN 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 GLU* 2.8 19.0 + - - +
108A GLU* 3.4 27.2 - - - +
110A TYR* 1.3 71.1 - - - +
112A LYS* 1.3 59.2 + - + +
113A GLY* 3.0 10.5 + - - -
127A LYS* 6.5 0.9 - - + -
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Residues in contact with LYS 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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85A MET* 4.1 37.9 - - + +
108A GLU* 2.8 17.0 + - + +
109A ALA* 3.9 6.7 - - - +
111A GLN* 1.3 76.4 - - + +
113A GLY* 1.3 55.2 + - - +
114A ILE* 3.3 19.4 + - + +
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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