Contacts of the helix formed by residues 97 - 114 (chain B) in PDB entry 2X1L
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 ASP 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 6.1 2.2 - - - +
91B ARG* 3.2 18.0 + - - +
92B PHE 4.6 2.3 - - - +
93B ILE* 3.9 2.4 - - - +
94B ARG* 3.0 45.7 + - - +
95B THR 3.3 0.2 - - - -
96B SER* 1.3 81.3 + - - +
98B ALA* 1.3 65.9 + - - +
99B ASP* 3.3 17.0 - - - +
100B HIS* 3.1 15.9 + - + +
101B TYR* 3.4 11.1 + - - -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 5.9 11.8 - - - +
96B SER 3.6 2.9 + - - -
97B ASP* 1.3 72.0 - - - +
99B ASP* 1.3 62.3 + - - +
101B TYR* 3.2 19.8 + - - +
102B GLU* 3.3 20.6 + - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 2.8 46.5 + - - -
97B ASP* 3.3 9.7 - - - +
98B ALA* 1.3 75.0 - - - +
100B HIS* 1.3 65.0 + - - +
102B GLU* 3.5 16.4 + - - +
103B ALA* 3.1 25.8 + - - +
239B THR* 3.7 10.6 - - + +
243B PHE 4.2 5.8 - - - +
244B PRO* 4.6 0.8 - - + +
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.4 3.4 - - + +
94B ARG 4.3 8.1 - - - +
95B THR* 3.3 30.7 - - + +
97B ASP* 3.1 11.5 + - + +
99B ASP* 1.3 81.7 + - - +
101B TYR* 1.3 59.6 + - - +
103B ALA* 3.7 0.2 - - - +
104B SER* 2.9 44.8 + - - -
217B VAL* 4.9 2.2 - - + -
232B ASP* 2.6 47.9 + - - -
235B THR* 3.7 2.2 - - - -
236B ASN* 3.3 31.3 - - + +
239B THR* 2.9 32.1 + - + -
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Residues in contact with TYR 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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52B HIS* 3.4 23.3 + + - -
95B THR 3.6 19.1 - - - -
96B SER* 3.8 17.1 - - - -
97B ASP 3.4 13.9 + - - -
98B ALA* 3.2 12.8 + - - +
100B HIS* 1.3 77.6 - - - +
102B GLU* 1.3 63.2 + - + +
104B SER* 3.5 1.8 + - - -
105B LYS* 3.1 44.8 + - - +
215B TRP* 5.2 5.4 - - - -
216B GLY 4.3 6.2 + - - -
217B VAL* 4.0 22.6 - - + +
218B PRO* 3.8 24.7 - - + -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 3.3 16.5 + - - +
99B ASP* 3.6 16.6 - - - +
101B TYR* 1.3 78.1 - - + +
103B ALA* 1.3 55.7 + - - +
105B LYS* 3.5 7.4 + - - +
106B ALA* 3.0 29.3 + - - +
244B PRO* 4.2 21.0 - - + +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP 3.1 11.2 + - - +
100B HIS 3.3 2.0 + - - +
102B GLU* 1.3 72.9 - - - +
104B SER* 1.3 65.0 + - - +
107B ILE* 3.1 23.2 + - - +
235B THR* 3.7 5.3 - - + +
239B THR* 3.3 26.9 - - - +
243B PHE* 3.4 46.1 - - + +
244B PRO* 4.0 4.7 - - - +
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Residues in contact with SER 104 (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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100B HIS* 2.9 43.3 + - - -
101B TYR 3.9 3.8 - - - -
103B ALA* 1.3 75.6 - - - +
105B LYS* 1.3 61.6 + - - +
107B ILE* 3.3 5.9 - - - +
108B TRP* 3.2 17.7 + - - +
217B VAL* 4.0 12.2 - - - +
227B MET* 3.3 29.8 - - - +
232B ASP* 4.0 11.4 + - - -
235B THR* 3.9 9.8 - - - +
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Residues in contact with LYS 105 (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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101B TYR* 3.1 35.7 + - - +
102B GLU* 3.8 6.5 - - - +
104B SER* 1.3 73.9 - - - +
106B ALA* 1.3 60.8 + - - +
108B TRP* 3.5 2.4 + - - +
109B LYS* 3.1 28.4 + - - +
217B VAL* 4.4 8.5 - - + -
218B PRO* 3.9 30.8 - - - +
220B PRO* 3.8 28.3 - - + +
227B MET* 3.9 8.7 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU 3.0 18.4 + - - +
103B ALA 3.7 4.5 - - - +
104B SER 3.3 0.2 - - - -
105B LYS* 1.3 76.8 - - - +
107B ILE* 1.3 57.3 + - - +
109B LYS* 3.4 8.9 + - - +
110B ARG* 3.0 32.7 + - - +
243B PHE* 3.8 8.1 - - + -
244B PRO* 3.6 27.4 - - + -
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Residues in contact with ILE 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 ALA 3.1 16.4 + - - +
104B SER 3.3 12.8 - - - +
106B ALA* 1.3 73.6 - - - +
108B TRP* 1.3 68.6 + - - +
110B ARG* 3.4 5.8 + - - +
111B MET* 3.0 37.8 + - + +
231B VAL* 5.2 4.7 - - + -
235B THR* 3.6 21.1 - - + +
238B LEU* 3.7 26.9 - - + -
243B PHE* 3.8 10.3 - - + -
274B TRP* 4.4 15.9 - - + -
277B PHE* 4.9 8.1 - - + +
278B LEU* 4.7 3.1 - - + -
281B ALA* 3.9 24.0 - - + -
283B LEU* 4.5 4.0 - - + -
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Residues in contact with TRP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B SER 3.2 18.2 + - - +
105B LYS* 3.7 5.2 - - - +
106B ALA 3.3 0.2 - - - -
107B ILE* 1.3 78.1 - - + +
109B LYS* 1.3 53.1 + - - +
111B MET* 3.3 10.3 + - + -
112B ALA* 2.8 36.8 + - + +
117B ILE* 3.5 20.8 - - + +
164B TYR* 4.1 16.7 - + + -
208B ILE* 3.3 57.9 - - + -
209B SER* 4.2 3.4 - - - -
219B VAL* 3.5 36.2 - - + +
220B PRO* 4.0 18.8 + - + -
227B MET* 3.6 35.4 - - + -
231B VAL* 4.2 13.7 - - + -
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Residues in contact with LYS 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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105B LYS 3.1 19.2 + - - +
106B ALA* 3.6 8.1 - - - +
108B TRP* 1.3 76.7 - - - +
110B ARG* 1.3 56.1 + - + +
112B ALA* 4.2 6.3 - - + -
113B ASP* 2.8 72.0 + - - +
220B PRO* 5.3 6.7 - - + +
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Residues in contact with ARG 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 ALA* 3.0 19.2 + - - +
107B ILE* 3.5 9.0 - - - +
108B TRP 3.3 0.2 - - - -
109B LYS* 1.3 76.7 - - - +
111B MET* 1.3 56.4 + - - +
113B ASP* 3.5 5.5 + - - +
114B ALA* 3.1 28.4 + - - +
243B PHE* 3.8 29.4 - - - -
244B PRO 5.5 1.0 + - - -
246B THR* 4.4 20.0 - - - +
280B SER 4.1 3.5 - - - +
281B ALA* 2.8 49.6 + - - +
282B GLY 4.2 4.9 + - - -
283B LEU* 3.7 23.7 - - - +
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Residues in contact with MET 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 ILE* 3.0 32.0 + - + +
108B TRP* 3.7 17.0 - - + +
110B ARG* 1.3 75.5 - - - +
112B ALA* 1.3 59.1 + - - +
114B ALA* 3.6 1.4 + - - +
115B GLY 3.5 3.3 + - - -
116B ASP* 3.0 29.6 + - - +
117B ILE* 3.8 17.0 - - + -
166B PHE* 3.8 11.9 - - + -
208B ILE* 5.5 2.9 - - + -
231B VAL* 4.3 23.3 - - + -
277B PHE* 3.7 51.1 - - + +
280B SER* 3.5 21.1 - - - +
281B ALA* 4.2 5.4 - - + +
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Residues in contact with ALA 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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108B TRP* 2.8 25.3 + - + +
109B LYS* 3.6 8.5 - - + +
111B MET* 1.3 74.8 - - - +
113B ASP* 1.3 62.9 + - - +
115B GLY* 3.0 19.4 + - - -
116B ASP 4.3 0.2 + - - -
117B ILE* 3.6 22.9 + - + +
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Residues in contact with ASP 113 (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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109B LYS* 2.8 56.9 + - - +
110B ARG* 3.9 5.9 - - - +
112B ALA* 1.3 75.7 - - - +
114B ALA* 1.3 60.4 + - - +
115B GLY* 3.1 1.1 + - - -
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Residues in contact with ALA 114 (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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110B ARG 3.1 18.2 + - - +
111B MET 3.7 7.2 - - - +
112B ALA 3.2 0.6 - - - -
113B ASP* 1.3 75.8 - - - +
115B GLY* 1.3 57.8 + - - +
116B ASP* 3.9 12.0 - - - +
280B SER* 3.5 20.9 - - - +
602B CXS 3.3 19.1 - - - +
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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
------------------------------------------------------------
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