Contacts of the helix formed by residues 107 - 122 (chain B) in PDB entry 1AHF
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B THR* 2.9 28.0 + - - -
106B PRO* 1.3 69.9 - - - +
108B GLY* 1.3 62.3 + - - -
109B SER 2.9 6.6 + - - -
110B GLY 3.2 6.1 + - - -
111B ALA 3.3 0.9 + - - -
266B ARG* 3.3 15.5 - - - -
267B VAL 3.8 16.2 - - - -
268B GLY* 3.6 6.2 - - - +
412B PLP 3.7 12.6 - - - -
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLY* 1.3 71.7 - - - -
109B SER* 1.3 60.7 + - - +
111B ALA* 3.5 5.4 + - - +
112B LEU* 3.3 28.7 + - - +
222B ASP* 5.7 0.6 - - - +
253B ALA* 4.4 3.5 - - - +
254B SER 3.6 21.8 - - - -
255B SER* 3.8 5.9 - - - -
412B PLP 2.6 32.9 + - - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 5.0 0.7 + - - -
294A ASN 3.4 10.2 - - - +
295A TYR 3.9 20.6 - - - -
296A SER* 3.8 13.8 - - - -
108B GLY* 1.3 80.1 - - - +
110B GLY* 1.3 61.9 + - - +
112B LEU* 3.2 20.2 + - - +
113B ARG 3.2 9.5 + - - -
140B TRP* 3.8 20.3 - - - -
142B ASN* 4.7 5.9 + - - +
146B VAL* 5.1 3.7 - - - +
266B ARG* 4.0 0.9 - - - -
412B PLP 2.9 22.9 + - - -
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Residues in contact with GLY 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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294A ASN* 4.0 11.4 - - - -
295A TYR* 4.3 8.3 - - - +
105B THR* 4.1 7.4 - - - -
106B PRO* 3.3 22.5 + - - -
107B GLY 3.2 4.6 + - - -
109B SER* 1.3 80.2 - - - +
111B ALA* 1.3 57.5 + - - +
113B ARG* 3.6 3.5 + - - +
114B VAL* 3.0 32.9 + - - +
294B ASN* 5.6 0.2 - - - +
295B TYR* 5.2 2.6 - - - -
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Residues in contact with ALA 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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105B THR* 3.4 25.7 + - - +
107B GLY 3.3 5.3 + - - +
108B GLY* 3.6 11.9 - - - +
110B GLY* 1.3 78.3 - - - +
112B LEU* 1.3 58.0 + - - +
114B VAL* 3.8 3.1 - - - -
115B ALA* 3.2 18.9 + - - +
253B ALA* 4.1 10.6 - - + +
269B ALA 3.5 26.2 - - - +
270B CYS* 3.4 16.8 - - + +
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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
----------------------------------------------------------
108B GLY 3.3 15.5 - - - +
109B SER* 3.2 10.5 + - - +
111B ALA* 1.3 77.1 - - - +
113B ARG* 1.3 67.3 + - - +
115B ALA* 3.3 3.4 + - + +
116B ALA* 2.9 23.9 + - - +
140B TRP* 3.8 14.6 - - + -
143B HIS* 3.7 18.8 - - + -
146B VAL* 3.9 18.1 - - + +
147B PHE* 4.2 20.6 - - + -
187B LEU* 4.9 3.4 - - + -
220B LEU* 4.8 12.8 - - + -
222B ASP* 3.6 27.4 - - + +
253B ALA* 3.5 22.2 - - + -
412B PLP 4.5 2.0 - - + -
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Residues in contact with ARG 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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113A ARG* 2.9 33.9 - - - +
117A ASP* 3.7 19.0 + - - -
290A ALA 4.4 3.0 + - - -
293A ALA* 3.0 30.4 + - - +
294A ASN* 3.6 44.5 - - - +
109B SER 3.2 3.2 + - - +
110B GLY 3.8 6.3 - - - +
112B LEU* 1.3 79.7 - - - +
114B VAL* 1.3 58.6 + - - +
116B ALA* 3.0 8.1 + - - +
117B ASP* 2.9 46.9 + - - +
146B VAL* 3.9 12.6 + - + +
149B SER* 3.7 28.1 + - - -
150B ALA* 5.0 0.4 - - - -
294B ASN* 4.3 5.6 + - - +
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Residues in contact with VAL 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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105B THR* 4.8 2.9 - - + -
110B GLY 3.0 22.1 + - - +
111B ALA* 4.1 6.7 - - - +
112B LEU 3.3 0.2 - - - -
113B ARG* 1.3 76.6 - - - +
115B ALA* 1.3 62.4 + - - +
117B ASP* 3.9 7.0 - - - +
118B PHE* 2.9 21.8 + - - +
270B CYS* 4.6 5.8 - - + -
287B MET* 3.7 36.6 - - + +
290B ALA* 4.6 5.5 - - + +
291B ILE* 3.7 33.9 - - + +
294B ASN* 4.8 7.2 - - + +
295B TYR* 4.1 18.2 - - + +
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Residues in contact with ALA 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 ALA 3.2 17.1 + - - +
112B LEU* 3.7 5.8 - - + +
113B ARG 3.2 0.4 - - - -
114B VAL* 1.3 79.5 - - - +
116B ALA* 1.3 53.1 + - - +
118B PHE* 3.0 10.1 + - - +
119B LEU* 2.8 41.0 + - + +
220B LEU* 4.4 15.5 - - + -
251B ILE* 4.1 20.4 - - + -
270B CYS* 4.0 14.4 - - - -
287B MET* 5.2 0.7 - - - -
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Residues in contact with ALA 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 14.5 + - - +
113B ARG* 3.1 14.4 - - - +
115B ALA* 1.3 77.2 - - - +
117B ASP* 1.3 57.4 + - - +
118B PHE 3.1 0.2 + - - -
119B LEU* 3.2 7.0 + - - +
120B ALA* 2.9 31.5 + - - +
146B VAL* 4.3 5.6 - - + +
147B PHE* 3.9 24.6 - - + -
150B ALA* 3.7 19.5 - - + -
152B LEU* 3.7 5.5 - - - +
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Residues in contact with ASP 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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113A ARG* 3.2 26.3 + - - -
113B ARG* 2.9 45.6 + - - +
114B VAL* 4.0 6.0 - - - +
116B ALA* 1.3 72.3 - - - +
118B PHE* 1.3 63.6 + - - +
120B ALA* 3.9 0.7 - - - +
121B LYS* 2.5 50.9 + - + +
122B ASN* 4.8 0.2 + - - -
150B ALA* 3.6 14.7 - - - +
290B ALA* 4.3 17.9 - - + +
294B ASN* 4.7 3.6 - - - +
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Residues in contact with PHE 118 (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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6A PHE* 4.0 16.6 - + - -
9A ILE* 4.0 12.8 - - + -
114B VAL 2.9 20.5 + - - +
115B ALA* 3.4 9.0 - - - +
116B ALA 3.0 0.2 - - - -
117B ASP* 1.3 79.9 - - - +
119B LEU* 1.3 63.6 - - + +
122B ASN* 2.7 62.4 + - + +
123B THR* 5.0 1.6 - - + -
251B ILE* 4.9 2.2 - - + -
272B LEU* 3.7 37.9 - - + -
283B ALA* 3.3 33.4 - - + -
286B GLN* 3.9 7.4 - - + -
287B MET* 3.6 34.3 - - + -
290B ALA* 4.7 4.9 - - + -
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Residues in contact with LEU 119 (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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6A PHE* 4.7 3.4 - - + -
115B ALA 2.8 19.2 + - - +
116B ALA* 3.4 7.6 - - - +
118B PHE* 1.3 85.8 - - + +
120B ALA* 1.3 64.9 + - - +
123B THR* 2.9 38.8 + - + +
125B VAL* 3.8 23.0 + - + -
133B VAL* 5.6 2.2 - - + -
147B PHE* 5.6 3.4 - - + -
152B LEU* 4.6 7.9 - - + -
185B VAL* 3.5 28.7 - - + -
218B LEU* 3.8 12.1 - - + -
220B LEU* 4.8 8.1 - - + -
251B ILE* 3.5 33.0 - - + -
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Residues in contact with ALA 120 (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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116B ALA 2.9 20.1 + - - +
117B ASP* 4.4 2.7 - - - +
119B LEU* 1.3 73.6 - - - +
121B LYS* 1.3 66.2 + - + +
123B THR 4.3 5.8 - - - +
125B VAL 5.1 2.7 - - - -
150B ALA* 3.2 30.7 - - + +
152B LEU* 3.8 20.2 - - + +
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Residues in contact with LYS 121 (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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113A ARG* 5.5 2.5 - - - +
149A SER* 3.8 30.8 + - - +
117B ASP* 2.5 58.6 + - + +
119B LEU 3.1 0.4 - - - -
120B ALA* 1.3 88.6 - - + +
122B ASN* 1.3 73.1 + - - +
123B THR 3.6 1.3 - - - -
150B ALA* 5.9 2.2 - - - +
290B ALA* 5.5 4.9 - - + -
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Residues in contact with ASN 122 (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 MET 5.0 0.5 - - - +
8A ASN* 5.2 1.9 - - - +
9A ILE* 3.7 31.8 - - + +
118B PHE* 2.7 38.8 + - + +
121B LYS* 1.3 89.7 - - - +
123B THR* 1.3 68.6 + - + +
286B GLN* 3.3 48.1 + - - +
290B ALA* 5.8 1.0 - - - +
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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