Contacts of the helix formed by residues 134 - 149 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H GLN 3.5 0.6 - - - -
133H GLN* 1.3 78.1 - - - +
135H LYS* 1.3 56.6 - - - +
137H SER* 3.2 9.1 + - - -
138H VAL* 3.1 33.1 + - - +
403H COT 2.7 24.2 + - - -
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Residues in contact with LYS 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H TRP* 2.9 79.7 - - + +
86H VAL* 3.4 10.8 - - - +
91H VAL* 3.6 9.1 - - - +
92H ALA* 5.3 4.9 - - + +
126H VAL* 4.9 6.3 - - + -
130H PHE* 3.7 37.2 - - + +
133H GLN* 3.3 32.5 - - + +
134H GLY* 1.3 75.5 - - - +
136H GLY* 1.3 64.6 + - - +
138H VAL 3.4 0.2 + - - -
139H LEU* 3.1 23.7 + - - +
403H COT 4.1 1.5 + - - +
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Residues in contact with GLY 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ALA* 5.6 0.2 - - - -
124H LEU* 4.7 6.2 - - - +
126H VAL* 3.6 18.5 - - - +
135H LYS* 1.3 76.1 - - - +
137H SER* 1.3 56.9 + - - +
139H LEU* 3.5 8.1 + - - +
140H LEU* 3.0 28.9 + - - +
167H PHE* 4.9 5.5 - - - -
403H COT 2.9 30.4 + - - -
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Residues in contact with SER 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H GLY* 3.2 8.4 + - - -
136H GLY* 1.3 74.5 - - - +
138H VAL* 1.3 60.1 + - - +
141H TRP* 2.9 40.2 + - - +
167H PHE* 3.7 5.4 - - - -
170H ARG* 5.1 2.4 + - - -
171H PHE* 3.6 30.6 - - - -
403H COT 2.7 28.1 + - - -
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Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLN* 3.8 33.2 - - + +
37H PHE* 3.5 15.9 - - + -
84H TRP* 3.3 33.9 - - + -
134H GLY 3.1 16.4 + - - +
135H LYS 3.8 0.9 - - - +
137H SER* 1.3 75.8 - - - +
139H LEU* 1.3 58.4 + - - +
141H TRP* 3.9 6.5 - - - +
142H ARG* 3.0 36.9 + - - +
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Residues in contact with LEU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.8 19.2 - - + -
82H LEU* 3.8 38.1 - - + +
83H GLY* 4.5 1.3 - - - +
84H TRP* 4.5 9.4 - - + +
92H ALA* 3.9 11.4 - - + -
93H PHE* 3.6 40.8 - - - +
94H ILE* 3.7 14.4 - - + -
124H LEU* 4.0 9.0 - - + -
126H VAL* 5.7 0.2 - - + -
135H LYS 3.1 16.9 + - - +
136H GLY* 3.5 4.9 - - - +
138H VAL* 1.3 75.1 - - - +
140H LEU* 1.3 59.2 + - - +
142H ARG* 3.1 3.5 + - - +
143H TYR* 2.8 27.0 + - - +
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Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H ILE* 3.9 15.0 - - + +
121H LEU* 3.6 31.2 - - + -
124H LEU* 4.3 9.4 - - + -
136H GLY 3.0 17.8 + - - +
137H SER 3.8 2.9 - - - +
139H LEU* 1.3 75.5 - - - +
141H TRP* 1.3 64.1 + - - +
143H TYR* 3.2 3.0 + - + +
144H LEU* 3.0 34.2 + - + +
167H PHE* 4.6 2.0 - - + -
168H TYR* 3.7 26.9 - - + -
171H PHE* 3.6 44.4 - - + -
173H PHE* 4.4 10.1 - - + -
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Residues in contact with TRP 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LYS* 3.3 38.2 - - + +
22G GLY* 3.8 12.6 - - - -
24G PRO* 3.6 36.6 - - + -
137H SER* 2.9 26.9 + - - +
138H VAL* 3.9 6.7 - - - +
140H LEU* 1.3 75.9 - - - +
142H ARG* 1.3 63.8 + - - +
144H LEU* 3.1 18.1 + - + +
145H HIS* 3.1 30.8 + - + -
170H ARG 3.5 18.9 + - - -
171H PHE* 3.7 43.8 - + - -
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Residues in contact with ARG 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.2 56.7 - - + +
82H LEU* 3.9 11.0 - - + -
138H VAL* 3.0 25.3 + - - +
139H LEU* 3.2 8.3 - - - +
141H TRP* 1.3 76.4 - - - +
143H TYR* 1.3 56.9 + - - +
145H HIS* 3.1 10.7 + - - +
146H HIS* 2.9 28.2 + - + +
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Residues in contact with TYR 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU* 2.7 39.9 + - - +
81H SER* 4.1 3.8 - - - -
82H LEU* 3.8 26.9 - - + +
94H ILE* 3.6 34.1 - - + -
96H GLY* 3.6 13.7 - - - -
97H SER 4.6 0.2 + - - -
119H ALA* 4.4 8.9 - - + +
120H HIS 4.6 1.0 + - - -
121H LEU* 3.6 36.0 - - + +
139H LEU 2.8 19.3 + - - +
140H LEU* 3.2 4.7 + - + +
142H ARG* 1.3 69.5 - - - +
144H LEU* 1.3 65.6 + - + +
146H HIS* 3.6 5.5 - + - +
147H VAL* 3.0 61.8 + - + +
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Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G PRO* 3.1 32.2 - - + +
121H LEU* 5.3 0.7 - - + -
140H LEU* 3.0 25.3 + - + +
141H TRP* 3.1 19.7 + - + +
143H TYR* 1.3 84.4 - - + +
145H HIS* 1.3 57.6 + - - +
147H VAL* 4.1 3.8 - - + -
148H GLY* 2.9 22.9 + - - -
156H ALA* 3.9 28.0 - - + -
171H PHE* 3.8 34.1 - - + +
173H PHE* 4.1 16.8 - - + -
193H CYS* 4.4 4.5 - - - -
195H LEU* 3.7 9.1 - - + +
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Residues in contact with HIS 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLY* 5.5 3.8 - - - -
20G ILE 3.2 35.7 + - - -
21G PRO* 4.3 3.8 - - + +
22G GLY 3.9 11.9 + - - -
23G SER 3.8 1.3 + - - -
24G PRO* 3.4 38.4 + - + +
141H TRP* 3.1 33.6 + + + +
142H ARG* 3.1 10.6 + - - +
144H LEU* 1.3 76.8 - - - +
146H HIS* 1.3 64.2 + - - +
149H ALA* 3.1 25.5 + - - +
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Residues in contact with HIS 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H CYS* 3.8 23.8 - - - -
79H GLU* 2.8 30.9 + - + -
81H SER 4.4 8.7 - - - -
82H LEU* 4.6 17.1 - - + +
142H ARG* 2.9 17.1 + - + +
143H TYR* 3.6 12.6 - + - +
145H HIS* 1.3 80.3 - - - +
147H VAL* 1.3 68.6 + - + +
149H ALA* 3.6 13.0 + - - +
150H GLN* 3.4 22.4 + - - +
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Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H GLU 4.5 1.3 - - - +
80H LEU* 4.1 17.9 - - + -
119H ALA* 3.9 22.9 - - + -
143H TYR* 3.0 58.2 + - + +
144H LEU* 3.9 9.4 - - + +
146H HIS* 1.3 82.7 - - + +
148H GLY* 1.3 67.8 + - - +
149H ALA 3.1 2.7 - - - -
150H GLN* 3.0 28.7 + - - +
153H VAL* 3.4 15.1 - - + +
195H LEU* 4.4 7.2 - - + -
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Residues in contact with GLY 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLY* 3.6 23.5 - - - +
144H LEU 2.9 23.2 + - - -
145H HIS 3.9 1.1 - - - -
146H HIS 3.4 0.2 - - - -
147H VAL* 1.3 78.0 - - - +
149H ALA* 1.3 60.8 + - - +
150H GLN 3.5 0.5 + - - -
153H VAL 4.4 1.8 - - - -
195H LEU* 3.9 14.6 - - - -
196H ARG* 3.4 26.9 - - - +
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Residues in contact with ALA 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G PRO 4.3 1.3 + - - +
25G GLY 5.6 0.9 - - - -
145H HIS 3.1 17.4 + - - +
146H HIS* 3.6 8.5 - - - +
147H VAL 3.1 0.2 - - - -
148H GLY* 1.3 75.5 - - - +
150H GLN* 1.3 62.6 + - + +
151H PRO* 3.3 9.7 - - - +
196H 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
------------------------------------------------------------
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