Contacts of the helix formed by residues 96 - 112 (chain B) in PDB entry 1XVI
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 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 5.6 1.8 - - - -
93B SER 4.6 4.0 - - - -
94B GLY 3.5 1.9 + - - -
95B ILE* 1.3 76.5 - - - +
97B HIS* 1.3 64.7 + - - +
98B GLY* 3.5 5.4 + - - -
99B GLU* 2.8 41.3 + - - +
100B ILE* 3.2 23.0 + - - +
144B GLU 3.5 11.4 - - - -
145B ALA* 4.0 2.2 - - - +
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B SER* 1.3 72.0 - - - +
98B GLY* 1.3 61.5 + - - +
100B ILE* 3.4 4.6 + - - +
101B SER* 2.9 45.4 + - - -
119B ASP* 2.9 42.1 + - - -
141B GLN 5.2 2.1 + - - -
143B HIS* 3.5 31.9 + + + +
144B GLU 2.8 23.2 + - - +
145B ALA* 3.6 0.6 - - - +
146B SER 3.1 29.4 + - - +
147B VAL* 3.7 3.0 - - + +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B SER* 3.2 7.5 + - - -
97B HIS* 1.3 85.7 - - - +
99B GLU* 1.3 56.3 + - - +
101B SER* 3.4 6.7 + - - -
102B LEU* 3.0 32.3 + - - +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY 2.9 24.3 - - - +
95B ILE* 3.8 13.7 - - + +
96B SER* 2.8 40.3 + - - +
98B GLY* 1.3 71.3 - - - +
100B ILE* 1.3 57.6 + - - +
102B LEU* 3.3 15.5 + - + +
103B VAL* 3.1 33.5 + - + +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 3.8 21.1 - - + +
96B SER 3.2 17.7 + - - +
97B HIS 3.7 5.4 - - - +
99B GLU* 1.3 73.7 - - - +
101B SER* 1.3 60.2 + - - +
103B VAL* 3.2 8.7 + - - +
104B LEU* 2.8 32.1 + - + +
145B ALA 3.6 24.0 - - - +
146B SER* 3.7 14.6 - - - +
147B VAL* 3.7 20.6 - - + -
170B LEU* 4.1 11.4 - - + -
181B VAL* 3.6 33.0 - - + +
182B LEU* 4.0 7.9 - - - -
183B ASP 4.7 0.7 - - - +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B HIS* 2.9 41.7 + - - -
98B GLY* 3.6 8.3 - - - -
99B GLU 3.4 0.2 - - - -
100B ILE* 1.3 76.8 - - - +
102B LEU* 1.3 55.5 + - - +
104B LEU* 3.8 6.1 - - - +
105B ASN* 2.8 45.9 + - - +
119B ASP* 3.9 6.6 + - - +
147B VAL* 3.7 8.6 - - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A TYR* 5.8 4.5 - - - +
98B GLY 3.0 19.0 + - - +
99B GLU* 3.4 16.2 - - + +
101B SER* 1.3 76.0 - - - +
103B VAL* 1.3 57.2 + - + +
105B ASN* 3.5 5.3 + - + +
106B THR* 2.7 34.6 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 6.4 0.9 - - + -
99B GLU* 3.1 19.7 + - + +
100B ILE* 3.4 9.6 - - - +
102B LEU* 1.3 75.1 - - + +
104B LEU* 1.3 64.9 + - + +
106B THR* 3.3 6.5 + - - -
107B LEU* 3.1 33.6 + - + +
165B LEU* 4.4 3.6 - - + -
168B LEU* 3.9 31.6 - - + -
170B LEU* 3.9 24.9 - - + -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 2.8 28.1 + - + +
101B SER* 3.8 5.2 - - - +
103B VAL* 1.3 73.8 - - + +
105B ASN* 1.3 59.1 + - - +
107B LEU* 3.4 3.6 + - + +
108B ARG* 2.9 30.2 + - - +
115B PHE* 3.5 15.3 - - + -
117B THR* 4.2 12.1 - - + -
147B VAL* 3.4 40.4 - - + -
149B LEU* 4.3 7.6 - - + -
161B PHE* 3.5 32.1 - - + -
165B LEU* 3.9 18.4 - - + -
181B VAL* 4.3 10.1 - - + -
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.6 39.9 + - - +
206A ARG* 5.4 1.5 + - - +
101B SER* 2.8 36.0 + - - +
102B LEU* 3.9 6.1 - - + +
104B LEU* 1.3 75.4 - - - +
106B THR* 1.3 55.5 + - - +
108B ARG* 3.1 30.7 + - - +
109B GLU* 2.8 43.5 + - + +
120B ASP* 5.0 0.7 + - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 2.7 23.6 + - - +
103B VAL* 3.6 7.1 - - - -
105B ASN* 1.3 75.1 - - - +
107B LEU* 1.3 60.1 + - + +
109B GLU* 4.0 3.7 - - - +
110B LYS* 3.0 40.7 + - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 3.1 28.6 + - + +
104B LEU* 3.7 4.7 - - + +
105B ASN 3.3 0.2 - - - -
106B THR* 1.3 79.2 - - + +
108B ARG* 1.3 57.0 + - - +
110B LYS* 5.0 0.4 - - - -
111B GLU* 2.9 42.3 + - + +
112B HIS 3.5 0.7 + - - -
113B PHE* 3.7 19.7 - - + -
161B PHE* 3.9 27.8 - - + -
164B ARG* 3.3 47.1 - - + +
165B LEU* 3.9 21.3 - - + -
168B LEU* 4.9 4.5 - - + -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY 4.5 4.0 + - - -
205A LYS* 3.9 42.8 + - - +
104B LEU 2.9 17.1 + - - +
105B ASN* 3.1 26.7 + - - +
107B LEU* 1.3 75.2 - - - +
109B GLU* 1.3 63.3 + - - +
112B HIS* 3.0 31.6 + - - +
113B PHE 3.5 21.5 - - - +
115B PHE* 2.9 59.3 + - + -
116B THR* 4.0 0.4 - - - +
117B THR* 5.1 2.4 - - - +
120B ASP* 2.7 44.0 + - - -
152B ARG* 6.1 0.2 - - - +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLN* 3.1 18.9 - - - +
6A GLN* 3.1 38.6 + - + +
205A LYS* 2.7 35.3 + - - +
105B ASN* 2.8 27.4 + - - +
106B THR* 4.0 4.5 - - - +
108B ARG* 1.3 74.7 + - - +
110B LYS* 1.3 57.8 + - - +
112B HIS* 3.3 22.2 + - - -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 3.0 23.6 + - + +
107B LEU* 5.0 0.2 - - - -
109B GLU* 1.3 79.0 - - + +
111B GLU* 1.3 81.5 + - + +
112B HIS* 3.6 15.2 + - - -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 2.9 28.7 + - + +
110B LYS* 1.3 93.8 - - + +
112B HIS* 1.3 64.9 + - - +
113B PHE* 3.4 27.5 - - + -
157B ARG* 2.5 37.9 + - - -
160B GLN* 5.1 2.6 + - - -
164B ARG* 5.8 5.3 + - - +
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Residues in contact with HIS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU 3.5 0.2 + - - -
108B ARG* 3.0 16.2 + - - -
109B GLU 3.3 22.3 + - - -
110B LYS 3.6 11.2 + - - -
111B GLU* 1.3 83.3 - - - +
113B PHE* 1.3 65.0 + - - +
114B LYS* 3.4 12.5 + - - +
153B ASP* 4.1 1.2 - - - +
157B ARG* 3.4 8.1 + - - +
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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