Contacts of the helix formed by residues 118 - 130 (chain H) in PDB entry 7CR3
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 THR 118 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362G TYR* 3.4 28.7 - - + +
365G ARG* 5.0 3.2 + - - +
111H THR* 3.5 4.1 - - - +
117H LEU* 1.3 78.0 - - - +
119H ASP* 1.3 65.3 + - - +
120H GLU* 3.9 13.9 + - - -
121H GLU* 2.5 35.1 + - - +
122H VAL* 3.2 25.1 + - - +
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Residues in contact with ASP 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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107H ARG* 6.4 0.4 - - + -
111H THR* 5.1 1.1 - - - -
118H THR* 1.3 77.3 - - - +
120H GLU* 1.3 100.5 + - - +
121H GLU 3.2 0.2 - - - -
122H VAL* 3.2 8.9 - - + +
123H ASP* 2.9 44.6 + - - +
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Residues in contact with GLU 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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358G SER* 4.3 17.5 - - - +
365G ARG* 5.1 12.2 + - - +
118H THR* 3.9 13.6 + - - +
119H ASP* 1.3 110.2 + - - +
121H GLU* 1.3 58.3 + - + +
123H ASP* 3.5 6.0 + - - +
124H GLU* 2.9 33.6 + - - +
127H ARG* 4.5 6.8 + - - +
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Residues in contact with GLU 121 (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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344G TRP* 3.6 3.3 + - - +
358G SER* 4.3 7.0 - - - +
359G THR* 3.0 40.4 + - - +
362G TYR* 3.3 30.3 - - - +
365G ARG* 5.7 0.2 - - - +
117H LEU* 3.2 37.1 - - + +
118H THR* 2.5 39.6 + - - +
119H ASP 3.2 0.6 - - - -
120H GLU* 1.3 75.3 - - + +
122H VAL* 1.3 60.3 + - - +
124H GLU* 3.1 10.1 + - - +
125H MET* 2.9 30.0 + - - +
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Residues in contact with VAL 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU* 4.1 9.0 - - + +
107H ARG* 3.7 45.5 - - + +
110H MET* 4.1 12.8 - - + -
111H THR* 3.7 14.6 - - + -
117H LEU* 5.2 1.3 - - + +
118H THR 3.2 15.7 + - - +
119H ASP* 3.2 21.8 - - + +
121H GLU* 1.3 78.1 - - - +
123H ASP* 1.3 57.4 + - - +
125H MET* 3.1 20.9 + - + +
126H ILE* 3.0 34.3 + - + +
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Residues in contact with ASP 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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107H ARG* 3.0 37.0 + - - +
119H ASP* 2.9 33.2 + - - +
120H GLU* 3.8 4.1 + - - +
122H VAL* 1.3 74.8 - - - +
124H GLU* 1.3 58.2 - - - +
126H ILE* 3.2 7.9 + - - +
127H ARG* 2.9 64.4 + - - +
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Residues in contact with GLU 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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344G TRP* 3.5 22.6 - - + +
355G ASP* 5.7 1.0 - - - +
356G LEU* 5.5 6.4 - - - +
358G SER* 3.8 24.2 + - - +
120H GLU 2.9 18.4 + - - +
121H GLU* 3.1 10.5 + - - +
123H ASP* 1.3 73.5 - - - +
125H MET* 1.3 64.1 + - - +
127H ARG* 3.0 31.7 + - - +
128H GLU* 3.0 27.0 + - - +
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Residues in contact with MET 125 (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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340G ILE* 4.7 3.6 - - + +
341G GLN* 4.6 3.8 - - - +
344G TRP* 3.5 55.6 - - + -
106H LEU* 6.1 0.2 - - - -
110H MET* 3.7 45.1 - - + -
117H LEU* 3.7 22.7 - - + -
121H GLU 2.9 13.8 + - - +
122H VAL* 3.1 19.0 + - + +
124H GLU* 1.3 75.9 - - - +
126H ILE* 1.3 56.9 + - + +
128H GLU* 3.3 0.9 + - - +
129H ALA* 2.8 35.0 + - + +
142H PHE* 4.7 4.4 - - + -
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Residues in contact with ILE 126 (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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103H ALA* 4.0 21.3 - - + +
106H LEU* 3.8 25.8 - - + -
107H ARG* 3.3 44.6 - - + +
122H VAL* 3.0 20.2 + - + +
123H ASP* 3.2 15.0 + - - +
125H MET* 1.3 77.5 - - + +
127H ARG* 1.3 59.9 + - + +
129H ALA* 4.6 2.0 - - - -
130H ASP* 2.8 48.8 + - + +
135H GLY* 4.7 3.8 - - - -
137H VAL* 4.7 0.9 - - + -
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Residues in contact with ARG 127 (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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120H GLU* 4.5 7.1 + - - +
123H ASP* 2.9 49.4 + - - +
124H GLU* 3.0 39.2 + - - +
126H ILE* 1.3 77.5 - - + +
128H GLU* 1.3 61.3 + - - +
130H ASP 3.7 12.7 - - - +
131H ILE* 4.9 5.0 - - - +
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Residues in contact with GLU 128 (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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344G TRP* 3.5 25.1 - - + -
347G TYR* 3.3 9.2 + - + -
353G ARG* 2.5 50.3 + - - -
124H GLU* 3.0 18.0 + - - +
125H MET 3.9 1.3 - - - +
127H ARG* 1.3 80.9 - - - +
129H ALA* 1.3 57.9 + - - +
131H ILE* 3.3 9.1 - - - +
142H PHE* 3.3 16.8 - - + -
145H MET* 3.2 37.1 - - - +
146H MET* 3.9 5.4 - - - -
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Residues in contact with ALA 129 (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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90H PHE* 5.9 1.6 - - + -
106H LEU* 6.2 1.1 - - + -
125H MET* 2.8 20.0 + - + +
126H ILE* 4.2 2.0 - - - +
128H GLU* 1.3 75.5 - - - +
130H ASP* 1.3 61.1 + - - +
131H ILE* 3.0 10.6 + - - +
137H VAL* 3.5 21.3 - - + +
141H GLU* 2.9 24.3 - - - +
142H PHE* 3.4 33.8 - - + +
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Residues in contact with ASP 130 (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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126H ILE* 2.8 28.2 + - + +
127H ARG* 3.7 9.2 - - - +
129H ALA* 1.3 70.6 - - - +
131H ILE* 1.3 64.1 + - - +
132H ASP* 2.8 24.4 - - - +
133H GLY* 3.1 8.9 + - - -
134H ASP* 2.4 23.6 + - - +
135H GLY* 2.4 33.8 + - - -
136H GLN 3.8 6.8 - - - +
137H VAL* 3.5 22.3 - - + +
141H GLU* 3.8 5.0 - - - +
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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