Contacts of the helix formed by residues 92 - 105 (chain C) in PDB entry 4QUG
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 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C HIS* 4.3 12.6 - - + +
90C ASP 4.0 1.3 + - - +
91C LEU* 1.3 76.0 - - - +
93C ARG* 1.3 65.2 + - - +
94C GLU* 3.5 13.1 + - - +
95C GLU* 2.9 42.2 + - - +
96C ILE* 2.9 20.4 + - - +
129C GLY* 3.9 0.2 - - - -
130C THR* 3.4 16.4 + - - +
131C ASN* 3.3 20.6 - - - +
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Residues in contact with ARG 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR* 1.3 71.5 - - - +
94C GLU* 1.3 80.3 + - - +
96C ILE* 3.4 7.2 + - - +
97C VAL* 3.1 28.9 + - - +
129C GLY* 3.6 9.8 - - - -
131C ASN* 2.8 29.3 + - - +
132C GLY* 3.5 25.1 - - - +
133C PRO* 2.9 42.6 + - - +
134C VAL* 4.0 16.8 - - + +
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR* 3.5 9.0 + - - +
93C ARG* 1.3 87.7 + - + +
95C GLU* 1.3 60.8 + - + +
97C VAL* 3.2 7.5 + - - +
98C GLU* 2.9 31.3 + - - +
131C ASN* 3.0 30.3 + - - -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP 4.1 3.3 - - - +
91C LEU* 3.4 27.6 - - + +
92C THR* 2.9 46.9 + - - +
94C GLU* 1.3 77.1 - - + +
96C ILE* 1.3 58.3 + - - +
98C GLU* 3.8 13.4 - - - +
99C LEU* 2.8 33.5 + - - +
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ILE* 4.2 27.4 - - + -
52C ASN* 3.9 12.8 - - - +
91C LEU* 3.8 17.9 - - + -
92C THR 2.9 13.3 + - - +
93C ARG* 3.6 8.5 - - - +
95C GLU* 1.3 76.9 - - - +
97C VAL* 1.3 63.0 + - - +
99C LEU* 3.3 2.4 + - - +
100C MET* 3.0 26.8 + - + +
118C LEU* 5.1 2.0 - - + -
127C ILE* 4.9 7.4 - - + -
128C PHE 4.3 2.2 - - - +
129C GLY* 3.8 31.4 - - - +
134C VAL* 4.8 7.9 - - + -
139C ILE* 3.6 31.6 - - + -
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ARG 3.1 17.8 + - - +
94C GLU* 3.7 6.1 - - - +
96C ILE* 1.3 76.4 - - + +
98C GLU* 1.3 57.9 + - - +
100C MET* 3.4 1.5 + - - -
101C ARG* 2.9 50.3 + - - +
134C VAL* 3.9 24.5 - - + -
138C LYS* 4.0 21.1 - - + -
139C ILE* 5.0 5.6 - - + -
142C PHE* 3.8 20.5 - - + -
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLU 2.9 16.6 + - - +
95C GLU* 3.8 13.6 - - - +
97C VAL* 1.3 78.9 - - - +
99C LEU* 1.3 57.1 + - - +
101C ARG* 3.4 10.5 + - - +
102C ASP* 2.9 53.7 + - - +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.9 9.6 - - + -
50C ILE* 4.0 6.7 - - + -
86C ARG* 6.0 0.9 - - - +
88C LYS* 3.6 46.2 - - + +
91C LEU* 3.8 16.2 - - + -
95C GLU 2.8 19.2 + - - +
96C ILE 3.7 3.1 - - - +
98C GLU* 1.3 77.5 - - - +
100C MET* 1.3 75.4 + - + +
102C ASP* 3.3 6.8 + - + +
103C VAL* 2.9 48.8 + - + +
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Residues in contact with MET 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.9 22.2 - - + -
50C ILE* 4.0 9.9 - - + -
96C ILE* 3.0 25.8 + - + +
97C VAL* 3.9 2.0 - - - +
99C LEU* 1.3 98.6 - - + +
101C ARG* 1.3 67.3 + - - +
103C VAL* 3.4 4.7 + - + -
104C SER* 2.9 26.2 + - - -
114C PHE* 5.1 0.9 - - + -
116C CYS* 4.1 16.8 - - - -
139C ILE* 3.6 30.5 - - + +
142C PHE* 3.8 21.1 - - + -
143C PHE* 3.7 23.3 - - + -
158C PHE* 5.0 0.2 - - - -
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 2.9 38.6 + - - +
98C GLU* 3.6 11.7 - - - +
100C MET* 1.3 76.3 - - - +
102C ASP* 1.3 70.3 + - - +
104C SER* 2.7 22.1 + - - -
105C LYS* 3.1 34.5 - - + +
138C LYS* 4.7 8.3 - - - +
142C PHE* 3.7 30.6 - - + -
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Residues in contact with ASP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 2.9 41.8 + - - +
99C LEU* 3.8 7.5 - - + +
101C ARG* 1.3 83.3 - - - +
103C VAL* 1.3 64.9 + - + +
105C LYS* 3.1 18.2 + - - +
106C GLU* 3.4 15.6 + - - +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.9 15.0 - - + -
48C ILE* 4.3 10.5 - - + -
86C ARG* 4.2 17.3 - - - +
99C LEU* 2.9 41.6 + - + +
100C MET* 3.9 6.1 - - + +
102C ASP* 1.3 77.7 - - + +
104C SER* 1.3 61.1 + - - +
106C GLU* 3.1 15.6 + - - +
108C HIS* 2.8 24.4 + - + -
114C PHE* 3.6 35.7 - - + -
143C PHE* 4.1 5.4 - - + -
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Residues in contact with SER 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C MET 2.9 15.4 + - - -
101C ARG* 2.7 20.1 + - - -
103C VAL* 1.3 76.0 - - - +
105C LYS* 1.3 66.8 + - - +
106C GLU 3.3 3.0 + - - +
142C PHE* 3.5 39.2 + - - +
143C PHE* 3.8 17.2 - - - -
147C ARG 4.8 3.6 + - - +
148C CYS* 3.4 27.4 - - - +
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.1 39.4 + - + +
102C ASP* 3.1 10.9 + - - +
103C VAL 3.1 0.8 - - - -
104C SER* 1.3 80.8 - - - +
106C GLU* 1.3 65.9 + - - +
142C PHE* 6.1 1.3 - - - -
147C ARG 5.7 5.6 + - - +
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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