Contacts of the helix formed by residues 111 - 124 (chain H) in PDB entry 5I2D
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 GLU 111 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H GLY* 1.3 75.6 - - - +
112H LEU* 1.3 67.0 + - - +
113H ARG* 3.2 8.7 - - + +
114H ALA* 3.1 10.5 + - + +
115H ARG* 3.0 22.8 + - - +
42J G 3.4 19.4 - - - +
43J G 2.8 27.0 + - - +
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Residues in contact with LEU 112 (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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111H GLU* 1.3 74.3 - - - +
113H ARG* 1.3 56.9 + - - +
115H ARG* 3.3 19.0 + - - +
116H ILE* 2.9 54.5 + - + +
149H THR* 4.2 7.2 - - - +
151H SER* 3.5 30.3 - - - +
155H SER* 3.7 35.0 - - - +
156H VAL 4.3 1.8 - - - +
159H VAL* 3.8 20.0 - - + -
43J G 3.4 36.3 + - + +
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Residues in contact with ARG 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H GLU* 3.2 6.4 - - + +
112H LEU* 1.3 79.5 - - - +
114H ALA* 1.3 56.8 + - - +
116H ILE* 3.3 2.4 + - - +
117H ALA* 2.9 30.2 + - + +
159H VAL* 3.9 28.0 + - + +
162H ASP* 4.6 9.3 + - - +
163H LEU* 3.8 26.2 - - + +
166H GLU* 2.7 42.8 + - - -
168H LEU* 4.4 5.1 - - - +
187H GLU* 2.7 42.9 + - + +
43J G 5.0 0.8 + - - -
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Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H GLY* 4.2 9.9 - - - -
111H GLU* 3.1 20.1 + - + +
113H ARG* 1.3 79.4 - - - +
115H ARG* 1.3 58.2 - - - +
117H ALA* 3.4 2.1 + - - +
118H ARG* 2.9 41.7 + - - +
187H GLU* 3.3 27.8 - - - +
188H ALA* 3.9 3.4 - - - +
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Residues in contact with ARG 115 (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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106H HIS* 3.4 29.9 - - + +
107H LEU* 3.3 28.4 + - - +
108H GLN* 5.8 0.8 - - - +
109H THR 3.5 15.9 - - - +
110H GLY 3.1 20.9 + - - -
111H GLU* 3.0 19.4 + - - +
112H LEU* 3.8 25.4 - - - +
114H ALA* 1.3 75.4 - - - +
116H ILE* 1.3 57.8 + - - +
118H ARG* 3.5 3.3 + - - +
119H TYR* 2.9 31.0 + - - +
149H THR* 2.9 39.5 + - - +
150H ALA* 3.5 15.4 + - - +
151H SER* 4.5 1.2 - - - -
43J G 4.6 5.5 + - - -
44J C 4.6 6.7 + - - -
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Residues in contact with ILE 116 (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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112H LEU* 2.9 41.6 + - + +
113H ARG* 3.7 4.5 - - - +
115H ARG* 1.3 74.2 - - - +
117H ALA* 1.3 59.5 + - - +
119H TYR* 3.3 2.1 + - - +
120H LEU* 2.9 39.9 + - + +
145H ILE* 4.2 18.4 - - + -
149H THR* 4.1 7.9 - - + -
156H VAL* 4.0 22.9 - - + +
159H VAL* 3.7 28.7 - - + -
160H LEU* 3.7 25.8 - - + -
163H LEU* 4.5 7.0 - - + -
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Residues in contact with ALA 117 (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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113H ARG 2.9 18.2 + - - +
114H ALA 3.7 4.0 - - - +
116H ILE* 1.3 77.1 - - - +
118H ARG* 1.3 56.7 + - - +
120H LEU* 3.3 5.7 + - - +
121H LEU* 2.9 34.0 + - - +
163H LEU* 5.7 3.4 - - + -
184H LEU* 3.8 39.4 - - + +
187H GLU* 3.9 16.4 - - + -
188H ALA* 4.1 3.6 - - - +
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Residues in contact with ARG 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H HIS* 3.1 54.0 + - - +
109H THR* 3.2 38.0 + - - +
110H GLY* 4.9 0.6 - - - -
114H ALA* 2.9 25.1 + - - +
115H ARG* 3.7 8.6 - - - +
117H ALA* 1.3 76.9 - - - +
119H TYR* 1.3 57.0 + - - +
121H LEU* 3.4 5.3 + - + +
122H PHE* 2.9 28.4 + - - +
188H ALA* 3.1 30.1 + - + +
190H SER* 3.1 32.6 + - - +
191H ALA* 4.5 1.6 - - - -
192H LEU* 4.0 26.7 + - + +
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Residues in contact with TYR 119 (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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41H THR* 5.4 0.7 + - - +
44H HIS* 3.0 39.3 + + - -
68H MET* 4.2 12.1 - - - +
103H TYR* 5.4 0.9 - + - -
106H HIS* 4.3 10.5 - - + -
115H ARG 2.9 18.3 + - - +
116H ILE 3.8 3.1 - - - +
118H ARG* 1.3 73.3 - - - +
120H LEU* 1.3 62.2 + - + +
122H PHE* 3.3 13.1 + + + -
123H LEU* 2.9 65.0 + - + +
140H VAL* 4.8 1.7 - - + +
144H GLU 4.3 3.8 + - - -
145H ILE* 3.9 32.1 - - + -
148H ALA* 3.4 27.5 - - + +
149H THR* 3.9 13.9 - - + -
192H LEU* 5.4 3.8 - - + -
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Residues in contact with LEU 120 (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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116H ILE* 2.9 35.9 + - + +
117H ALA* 3.6 8.3 - - - +
119H TYR* 1.3 78.9 - - + +
121H LEU* 1.3 56.9 + - + +
123H LEU* 3.2 8.7 + - + +
124H ALA* 2.9 27.4 + - - +
138H VAL* 4.4 21.4 - - + +
140H VAL* 4.7 4.5 - - + -
145H ILE* 4.2 25.6 - - + -
160H LEU* 4.3 10.1 - - + -
163H LEU* 4.8 3.6 - - + -
169H ILE* 4.5 14.4 - - + -
176H VAL* 4.5 9.9 - - + -
178H LEU* 4.2 28.7 - - + +
184H LEU* 4.9 4.7 - - + -
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Residues in contact with LEU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 3.3 38.2 + - + +
117H ALA 2.9 19.8 + - - +
118H ARG* 3.8 4.7 - - + +
120H LEU* 1.3 77.5 - - - +
122H PHE* 1.3 61.9 + - - +
124H ALA* 3.3 17.0 + - + +
125H ASP* 3.4 14.0 - - - +
178H LEU* 4.4 3.8 - - + -
181H LEU* 4.1 26.7 - - + +
184H LEU* 3.5 50.0 - - + +
185H GLU* 3.7 9.9 - - - +
188H ALA* 4.0 11.4 - - + -
191H ALA* 6.5 0.7 - - - -
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Residues in contact with PHE 122 (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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44H HIS* 3.7 47.8 - + + -
46H LEU* 5.1 7.4 - - + -
99H ARG* 6.1 1.3 - - - -
118H ARG 2.9 18.1 + - - +
119H TYR* 3.5 23.6 - + - +
121H LEU* 1.3 75.6 - - - +
123H LEU* 1.3 67.9 + - + +
125H ASP* 3.0 22.1 + - - +
126H THR* 3.3 22.6 - - + +
192H LEU* 4.1 31.0 - - + +
193H GLU 3.8 22.7 - - - -
194H ALA* 3.9 20.2 - - + -
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Residues in contact with LEU 123 (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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27H LEU* 4.7 2.9 - - + -
44H HIS* 4.5 5.4 - - + +
68H MET* 5.1 0.2 - - + -
119H TYR* 2.9 67.7 + - + +
120H LEU* 3.6 9.2 - - + +
122H PHE* 1.3 81.4 - - + +
124H ALA* 1.3 61.0 + - - +
125H ASP 3.0 5.6 - - - -
126H THR* 2.6 30.5 + - + +
128H LEU* 4.0 18.1 - - + +
129H SER* 3.6 9.4 + - - -
138H VAL* 3.6 16.3 - - + +
140H VAL* 4.0 33.7 - - + -
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Residues in contact with ALA 124 (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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296A GLU* 2.6 34.7 + - + -
297A ARG* 4.6 16.8 - - + +
120H LEU 2.9 13.0 + - - +
121H LEU* 3.3 17.9 - - + +
122H PHE 3.1 0.4 - - - -
123H LEU* 1.3 77.3 - - - +
125H ASP* 1.3 51.6 + - - +
126H THR 3.4 0.7 - - - -
129H SER* 2.9 9.6 + - - -
136H ILE* 4.9 7.0 - - + -
138H VAL* 3.8 11.6 - - + +
178H LEU* 4.2 16.4 - - + -
181H LEU* 5.9 0.2 - - + -
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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