Contacts of the helix formed by residues 134 - 149 (chain F) in PDB entry 1IB1
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 134 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLN 3.5 0.4 - - - -
133F GLN* 1.3 79.0 - - - +
135F LYS* 1.3 57.7 + - - +
137F SER* 3.2 8.1 + - - -
138F VAL* 3.1 33.0 + - - +
400F COT 2.7 25.0 + - - -
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Residues in contact with LYS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F TRP* 2.9 80.0 - - + +
86F VAL* 3.5 9.8 - - + +
91F VAL* 3.6 8.9 - - - +
92F ALA* 5.2 4.4 - - + +
126F VAL* 4.8 6.3 - - + -
130F PHE* 3.7 37.7 - - + +
133F GLN* 3.1 33.0 - - + +
134F GLY* 1.3 76.0 - - - +
136F GLY* 1.3 65.0 + - - +
138F VAL 3.5 0.3 + - - -
139F LEU* 3.1 23.2 + - - +
400F COT 4.0 1.0 + - - +
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Residues in contact with GLY 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F LEU* 4.7 6.4 - - - +
126F VAL* 3.6 19.4 - - - +
134F GLY 3.3 0.2 - - - -
135F LYS* 1.3 76.1 - - - +
137F SER* 1.3 57.2 + - - +
139F LEU* 3.5 7.0 + - - +
140F LEU* 3.0 28.6 + - - +
167F PHE* 5.0 5.1 - - - -
400F COT 3.0 29.4 + - - -
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Residues in contact with SER 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F GLY* 3.2 7.3 + - - -
136F GLY* 1.3 75.3 - - - +
138F VAL* 1.3 59.9 + - - +
141F TRP* 2.9 40.4 + - - +
167F PHE* 3.7 6.2 - - - -
170F ARG* 5.1 2.4 + - - -
171F PHE* 3.6 30.4 - - - -
400F COT 2.7 28.6 + - - -
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.8 32.5 - - + +
37F PHE* 3.5 14.4 - - + -
84F TRP* 3.3 34.1 - - + -
134F GLY* 3.1 17.8 + - - +
135F LYS 3.8 0.2 - - - +
136F GLY 3.4 0.4 - - - -
137F SER* 1.3 76.5 - - - +
139F LEU* 1.3 57.1 + - - +
141F TRP* 3.8 6.7 - - - +
142F ARG* 2.9 38.1 + - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 3.8 19.9 - - + -
82F LEU* 3.7 39.3 - - + +
83F GLY* 4.5 0.7 - - - +
84F TRP* 4.4 9.0 - - + +
92F ALA* 3.9 10.8 - - + +
93F PHE 3.7 38.4 - - - +
94F ILE* 3.7 15.5 - - + -
124F LEU* 4.0 9.6 - - + -
135F LYS 3.1 16.9 + - - +
136F GLY* 3.5 5.4 - - - +
137F SER 3.2 0.2 - - - -
138F VAL* 1.3 74.9 - - - +
140F LEU* 1.3 59.9 + - - +
142F ARG* 3.2 3.1 + - - +
143F TYR* 2.8 26.9 + - - +
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ILE* 3.9 14.3 - - + +
121F LEU* 3.6 30.5 - - + -
124F LEU* 4.3 9.9 - - + -
136F GLY 3.0 17.8 + - - +
137F SER* 3.8 3.6 - - - +
139F LEU* 1.3 75.3 - - - +
141F TRP* 1.3 64.8 + - - +
143F TYR* 3.1 4.4 + - + +
144F LEU* 3.0 33.0 + - + +
167F PHE* 4.6 2.2 - - + -
168F TYR* 3.7 27.4 - - + -
171F PHE* 3.6 45.3 - - + -
173F PHE* 4.4 10.1 - - + -
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Residues in contact with TRP 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.5 35.7 - - + +
22E GLY* 3.9 21.1 - - - -
24E PRO* 3.6 35.9 - - + -
137F SER* 2.9 27.6 + - - +
138F VAL* 3.8 6.3 - - - +
140F LEU* 1.3 74.6 - - - +
142F ARG* 1.3 64.3 + - - +
144F LEU* 3.1 19.1 + - + +
145F HIS* 3.1 31.0 + - + +
170F ARG 3.6 13.3 + - - -
171F PHE* 3.7 40.9 - + - -
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Residues in contact with ARG 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 6.4 0.2 - - - +
37F PHE* 3.2 58.2 - - + +
82F LEU* 3.9 10.3 - - + -
138F VAL* 2.9 25.1 + - - +
139F LEU 3.2 7.0 - - - +
141F TRP* 1.3 77.2 - - - +
143F TYR* 1.3 55.2 + - - +
145F HIS* 3.1 9.8 + - - +
146F HIS* 2.9 28.9 + - + +
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Residues in contact with TYR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LEU* 2.7 39.7 + - - +
81F SER* 4.1 3.6 - - - -
82F LEU* 3.8 27.8 - - + +
94F ILE* 3.6 35.0 - - + -
96F GLY* 3.6 12.8 - - - -
97F SER 4.7 0.2 + - - -
119F ALA* 4.3 8.8 - - + +
120F HIS 4.6 1.0 + - - -
121F LEU* 3.6 33.8 - - + +
139F LEU 2.8 19.9 + - - +
140F LEU* 3.5 4.7 - - + +
142F ARG* 1.3 72.8 - - - +
144F LEU* 1.3 63.6 + - + +
146F HIS* 3.6 4.3 - + - +
147F VAL* 3.0 60.9 + - + +
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E PRO* 3.2 24.9 - - + +
121F LEU* 5.3 0.7 - - + -
140F LEU* 3.0 25.3 + - + +
141F TRP* 3.1 23.8 + - + +
143F TYR* 1.3 84.1 - - + +
145F HIS* 1.3 58.1 + - - +
147F VAL* 4.1 3.6 - - + -
148F GLY* 2.9 25.6 + - - -
156F ALA* 3.9 27.8 - - + -
171F PHE* 3.8 34.1 - - + +
173F PHE* 4.0 17.3 - - + -
193F CYS* 4.5 3.8 - - - -
195F LEU* 3.7 8.8 - - + +
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Residues in contact with HIS 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E GLY* 5.5 4.0 - - - -
20E ILE 3.4 34.3 + - - -
21E PRO* 4.4 3.4 - - + +
22E GLY 4.0 11.9 + - - -
23E SER 3.9 1.1 + - - -
24E PRO* 3.5 36.9 + - + +
141F TRP* 3.1 36.0 + + + -
142F ARG* 3.1 9.8 + - - +
144F LEU* 1.3 75.8 - - - +
146F HIS* 1.3 65.0 + - - +
149F ALA* 3.1 25.1 + - - +
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Residues in contact with HIS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F CYS* 3.8 24.4 - - - -
79F GLU* 2.9 30.5 + - + -
81F SER 4.1 9.6 + - - -
82F LEU* 4.6 15.9 - - + +
142F ARG* 2.9 16.9 + - + +
143F TYR* 3.6 12.1 - + - +
145F HIS* 1.3 79.1 - - - +
147F VAL* 1.3 68.2 + - + +
149F ALA* 3.6 12.5 - - - +
150F GLN* 3.4 21.9 + - - +
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Residues in contact with VAL 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F GLU 4.5 1.1 - - - +
80F LEU* 4.1 17.7 - - + -
119F ALA* 4.0 22.4 - - + -
143F TYR* 3.0 60.3 + - + +
144F LEU* 3.9 10.1 - - + +
146F HIS* 1.3 82.3 - - + +
148F GLY* 1.3 69.8 + - - +
149F ALA 3.1 2.0 - - - -
150F GLN* 3.0 28.0 + - - +
153F VAL* 3.4 14.3 - - + +
195F LEU* 4.4 7.9 - - + -
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Residues in contact with GLY 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E PRO 4.1 0.4 - - - -
25E GLY* 3.8 21.0 - - - +
144F LEU 2.9 23.3 + - - -
145F HIS 3.4 1.1 + - - -
147F VAL* 1.3 77.6 - - - +
149F ALA* 1.3 59.9 + - - +
150F GLN 3.4 0.7 + - - -
153F VAL 4.4 1.6 - - - -
195F LEU* 3.9 17.9 - - - -
196F ARG* 3.3 27.0 - - - +
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Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E PRO 4.4 1.9 + - - +
25E GLY 5.8 0.7 - - - -
145F HIS 3.1 17.1 + - - +
146F HIS* 3.6 8.5 - - - +
147F VAL 3.1 0.2 - - - -
148F GLY* 1.3 76.0 - - - +
150F GLN* 1.3 63.3 + - + +
151F PRO* 3.2 11.1 - - - +
196F ARG* 5.4 0.4 - - - -
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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
------------------------------------------------------------
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