Contacts of the helix formed by residues 100 - 117 (chain B) in PDB entry 1AX4
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 GLY 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN* 1.3 71.4 - - - +
101B ARG* 1.3 54.8 + - - +
103B ALA* 3.0 7.0 + - - +
104B GLU* 3.0 30.4 + - - +
261B THR* 5.1 1.2 - - - -
262B MET 3.8 8.1 - - - -
263B SER* 3.7 19.9 - - - +
266B LLP 2.8 33.9 + - - -
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Residues in contact with ARG 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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72A TYR* 3.2 20.4 + - - -
293A VAL* 2.7 47.2 + - - +
294A PRO 3.2 18.4 - - - +
295A MET 4.2 7.2 - - - -
296A GLU 4.4 0.7 - - - +
297A GLY* 3.5 24.3 - - - +
298A PHE* 3.9 3.0 - - - +
99B GLN* 3.3 15.6 - - + +
100B GLY* 1.3 69.4 - - - +
102B GLY* 1.4 62.3 + - - +
104B GLU* 3.5 10.3 - - - +
105B ASN* 2.9 28.4 + - - +
132B PHE* 5.2 3.2 - - - -
134B THR* 3.5 37.6 - - - +
138B HIS* 3.5 6.3 + - - +
266B LLP 2.7 45.2 + - - +
459B PHE* 5.7 2.4 - - - -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A MET 4.5 2.5 - - - -
97B ALA* 4.0 5.6 - - - -
98B HIS* 4.1 9.3 - - - -
99B GLN 3.1 9.6 + - - -
101B ARG* 1.4 81.3 - - - +
103B ALA* 1.3 62.5 + - - +
105B ASN* 3.3 6.0 + - - +
106B ILE* 3.2 27.7 + - - +
296B GLU* 3.6 25.2 - - - +
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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
----------------------------------------------------------
97B ALA* 3.7 8.4 - - + +
99B GLN 3.1 10.3 + - - +
100B GLY* 3.0 10.6 + - - +
102B GLY* 1.3 77.7 - - - +
104B GLU* 1.3 55.7 + - - +
106B ILE* 3.4 3.7 + - - +
107B LEU* 3.0 31.0 + - - +
261B THR* 4.3 6.1 - - - -
262B MET 4.4 7.9 - - - +
275B LEU 3.6 19.7 - - - +
276B VAL* 3.4 27.3 - - + +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLY 3.0 16.3 + - - +
101B ARG* 3.5 11.1 - - - +
103B ALA* 1.3 74.7 - - - +
105B ASN* 1.3 59.7 + - - +
108B PHE* 2.9 60.1 + - + +
134B THR* 2.6 28.8 + - - +
135B THR* 2.6 38.6 + - - +
138B HIS* 3.8 15.6 - - + -
223B ASP* 3.8 3.8 - - - +
261B THR* 4.5 12.7 + - + -
266B LLP 3.2 17.0 + - - -
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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
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105A ASN* 4.2 2.0 - - - +
295A MET* 3.5 34.1 + - - +
101B ARG 2.9 18.9 + - - +
102B GLY* 3.3 7.8 + - - +
104B GLU* 1.3 77.9 - - - +
106B ILE* 1.3 52.6 + - - +
109B PRO* 3.3 9.1 - - - +
138B HIS* 3.6 19.6 + - + -
142B ASN* 5.5 0.5 + - - -
291B ARG* 2.7 47.5 + - - -
295B MET* 3.5 35.9 - - - +
296B GLU* 5.1 3.8 + - - -
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Residues in contact with ILE 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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95B ILE* 4.2 11.7 - - + -
96B PRO 4.3 0.4 - - - +
97B ALA* 4.2 14.6 - - + -
102B GLY 3.2 14.9 + - - +
103B ALA* 3.6 7.9 - - - +
105B ASN* 1.3 75.6 - - - +
107B LEU* 1.3 65.5 + - + +
109B PRO* 4.2 0.2 - - - -
110B VAL* 3.4 22.5 + - - +
276B VAL* 4.3 12.8 - - + -
288B ALA* 3.6 33.9 - - + +
291B ARG* 3.8 13.1 - - - +
292B CYS* 4.0 31.2 - - + +
295B MET* 5.2 2.9 - - + -
296B GLU* 3.7 25.8 - - + -
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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 ALA 3.0 16.6 + - - +
106B ILE* 1.3 78.8 - - - +
108B PHE* 1.3 71.2 + - + +
109B PRO 3.4 0.2 - - - -
110B VAL* 3.1 6.5 + - + +
111B LEU* 3.0 31.6 + - + +
221B VAL* 4.1 25.6 - - + -
259B ALA* 4.4 13.0 - - + -
260B LEU 4.7 0.9 - - - +
261B THR* 3.8 22.2 - - + -
276B VAL* 4.6 21.5 - - + -
278B ILE* 4.7 3.8 - - + -
284B ILE* 3.9 28.0 - - + -
288B ALA* 4.6 8.5 - - + -
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU* 2.9 33.3 + - + +
107B LEU* 1.3 76.4 - - + +
109B PRO* 1.3 67.4 - - + +
111B LEU* 2.9 18.6 + - + +
112B LEU* 3.1 12.7 + - - +
126B PHE* 4.2 25.0 - + + -
135B THR* 3.4 39.3 - - + -
138B HIS* 4.1 23.3 - - + +
139B VAL* 4.1 19.1 - - + -
142B ASN* 4.9 6.7 - - + +
188B VAL* 4.3 15.3 - - + -
221B VAL* 4.5 13.7 - - + -
261B THR* 4.2 23.1 - - + -
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU 3.6 2.5 - - - +
105B ASN* 3.3 28.5 - - - +
106B ILE 4.2 0.4 - - - +
107B LEU 3.6 1.6 - - - -
108B PHE* 1.3 93.8 - - + +
110B VAL* 1.3 56.5 + - - +
112B LEU* 3.3 7.3 + - + +
113B LYS* 3.0 30.2 + - - +
138B HIS* 5.9 0.2 - - - +
142B ASN* 3.6 33.7 - - - +
291B ARG* 3.5 31.9 - - - +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE 3.4 17.7 - - - +
107B LEU* 3.1 10.9 + - + +
108B PHE 3.1 0.6 - - - -
109B PRO* 1.3 80.3 - - - +
111B LEU* 1.3 56.9 + - - +
113B LYS* 3.9 7.3 - - + +
114B TYR* 3.0 27.0 + - - +
284B ILE* 3.9 29.2 - - + +
287B LEU* 3.5 52.6 - - + +
288B ALA* 3.8 3.8 - - + +
291B ARG* 4.3 11.9 - - + -
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Residues in contact with LEU 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* 3.0 34.0 + - + +
108B PHE* 2.9 17.5 + - + +
110B VAL* 1.3 75.6 - - - +
112B LEU* 1.3 63.9 + - - +
114B TYR* 3.4 7.6 + - + +
115B LYS* 3.1 23.4 + - - +
126B PHE* 4.6 2.5 - - + -
185B VAL* 3.6 18.2 - - + +
186B ALA* 4.2 10.3 - - + -
219B PHE* 3.6 33.7 - - + -
221B VAL* 3.7 29.6 - - + -
284B ILE* 4.0 21.1 - - + -
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Residues in contact with LEU 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 PHE 3.1 11.0 + - - +
109B PRO* 3.6 9.2 - - + +
111B LEU* 1.3 73.6 - - - +
113B LYS* 1.3 65.9 + - - +
115B LYS* 3.0 5.1 + - - +
116B GLN* 2.9 56.0 + - + +
121B ALA* 4.3 1.3 - - + -
124B PRO* 3.8 29.6 - - + -
126B PHE* 5.4 1.3 - - + -
142B ASN* 3.3 37.2 - - + +
144B CYS* 4.0 11.2 - - - -
185B VAL* 3.6 16.9 - - + +
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Residues in contact with LYS 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 PRO 3.0 17.8 + - - +
110B VAL* 4.0 7.4 - - + +
112B LEU* 1.3 75.3 - - - +
114B TYR* 1.3 58.1 + - - +
116B GLN* 3.2 13.8 + - - +
117B LYS* 2.8 41.5 + - + +
287B LEU* 4.0 33.4 - - + +
290B GLN* 5.1 4.2 + - - -
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Residues in contact with TYR 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 VAL 3.0 20.2 + - - +
111B LEU* 3.5 7.6 - - + +
112B LEU 3.2 0.2 - - - -
113B LYS* 1.3 77.8 - - - +
115B LYS* 1.3 63.5 + - + +
117B LYS* 3.7 25.3 - - + +
118B GLU* 3.6 28.6 + - - -
219B PHE* 5.7 7.0 - + + -
281B ASN* 3.4 23.0 + - - -
283B GLU* 3.6 39.0 + - + -
284B ILE* 3.4 29.2 - - + -
287B LEU* 4.4 10.7 - - + +
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Residues in contact with LYS 115 (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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111B LEU 3.1 11.9 + - - +
112B LEU 3.0 8.6 + - - +
114B TYR* 1.3 80.7 - - + +
116B GLN* 1.3 62.2 + - - +
118B GLU* 3.5 22.5 + - - +
120B LYS* 3.4 29.8 + - + +
121B ALA* 3.7 20.6 - - + -
181B ALA 2.9 15.1 + - - -
182B ASP* 3.3 23.3 - - - +
184B ILE 2.8 28.0 + - - +
185B VAL* 4.5 18.5 + - + +
216B HIS 5.2 1.0 + - - -
217B GLY 4.2 17.2 + - - -
218B ILE* 4.3 6.5 - - - +
219B PHE 5.4 0.4 - - - +
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Residues in contact with GLN 116 (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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112B LEU* 2.9 40.5 + - + +
113B LYS* 3.6 16.2 - - - +
115B LYS* 1.3 72.5 - - - +
117B LYS* 1.3 56.1 + - - +
118B GLU 3.1 2.2 - - - -
119B GLY* 2.7 26.7 + - - -
120B LYS 3.6 11.2 - - - +
121B ALA* 3.8 22.8 + - + +
124B PRO* 5.4 2.0 - - - +
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Residues in contact with LYS 117 (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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113B LYS* 2.8 32.1 + - + +
114B TYR* 3.7 23.1 - - + +
115B LYS 3.4 0.2 - - - -
116B GLN* 1.3 71.8 - - - +
118B GLU* 1.3 69.9 + - + +
119B GLY* 3.3 1.0 + - - -
283B GLU* 3.4 26.0 + - - +
287B LEU* 4.0 22.4 - - - +
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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
------------------------------------------------------------
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