Contacts of the helix formed by residues 101 - 108 (chain C) in PDB entry 4G1U
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 SER 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.8 30.5 + - - +
99C PRO 3.9 2.0 + - - -
100C PHE* 1.3 73.9 - - - +
102C VAL* 1.3 66.8 + - - +
103C SER* 4.0 4.2 + - - -
104C GLU* 2.8 47.5 + - - +
105C VAL* 2.9 11.0 + - - +
135C ALA 4.1 9.4 - - - -
136C GLN* 4.3 6.9 + - - -
137C ARG 3.2 11.7 - - - -
138C ASP* 4.8 0.2 - - - +
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Residues in contact with VAL 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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100C PHE 3.8 0.4 + - - -
101C SER* 1.3 70.8 - - - +
103C SER* 1.3 56.5 + - - +
105C VAL* 3.1 10.1 + - - +
106C ILE* 2.9 45.9 + - + +
126C MET* 5.0 2.0 - - + -
131C CYS* 5.2 1.1 - - + -
134C LEU* 3.2 33.9 - - + +
135C ALA* 3.7 4.4 + - - +
137C ARG* 3.0 20.5 + - + +
139C TYR* 4.5 5.4 - - - -
142C LEU* 3.5 31.0 - - + -
150C VAL* 3.6 30.5 - - + -
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Residues in contact with SER 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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101C SER* 4.2 4.5 - - - -
102C VAL* 1.3 77.8 - - - +
104C GLU* 1.3 57.0 + - - +
106C ILE* 3.4 6.5 + - - +
107C GLN* 2.9 32.9 + - - +
122C LEU* 4.0 11.0 - - - +
126C MET* 4.5 4.9 - - - +
135C ALA* 2.7 41.2 + - - +
136C GLN* 3.8 13.3 + - - -
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Residues in contact with GLU 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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4B ARG* 6.1 1.1 - - - -
273B GLY* 4.3 14.0 - - - -
275B ASP* 4.2 21.3 - - - +
99C PRO 4.1 3.1 - - - +
100C PHE* 3.3 27.2 - - + -
101C SER* 2.8 41.2 + - - +
103C SER* 1.3 74.9 - - - +
105C VAL* 1.3 58.5 + - - +
107C GLN* 3.4 7.5 + - - +
108C MET* 2.9 32.9 + - + +
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Residues in contact with VAL 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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220B LEU* 4.6 8.5 - - + -
96C LEU* 3.8 11.0 - - + -
100C PHE* 3.7 22.0 - - + -
101C SER 2.9 16.4 + - - +
102C VAL 3.1 8.0 + - - +
104C GLU* 1.3 76.4 - - - +
106C ILE* 1.3 58.5 + - - +
108C MET* 3.1 27.3 - - + +
139C TYR* 3.6 42.6 - - + -
150C VAL* 4.4 5.8 - - + -
151C GLN* 4.4 5.2 - - - +
154C ARG* 3.4 24.6 - - + -
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Residues in contact with ILE 106 (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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102C VAL* 2.9 32.6 + - + +
103C SER 4.0 2.5 - - - +
105C VAL* 1.3 72.7 - - - +
107C GLN* 1.3 58.1 + - - +
108C MET 3.0 1.8 - - - -
109C GLY* 2.7 27.9 + - - -
110C ARG 3.9 1.4 + - - -
122C LEU* 3.9 16.4 - - + -
125C VAL* 4.8 0.9 - - + -
126C MET* 3.6 32.5 - - + -
131C CYS* 4.4 3.4 - - - -
150C VAL* 4.1 18.4 - - + +
153C ALA* 3.7 37.2 - - + +
154C ARG* 4.2 6.8 - - - +
157C ALA* 3.9 15.3 - - + +
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Residues in contact with GLN 107 (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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103C SER 2.9 19.5 + - - +
104C GLU* 3.7 7.9 - - - +
106C ILE* 1.3 71.8 - - - +
108C MET* 1.3 57.7 + - - +
109C GLY 3.0 4.9 - - - -
110C ARG* 2.9 20.4 + - - +
111C ALA 4.1 1.6 + - - -
118C ASP* 2.8 44.9 + - - +
122C LEU* 3.8 25.8 - - + +
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Residues in contact with MET 108 (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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216B ASN* 3.6 36.8 - - - +
217B LEU* 3.4 24.3 - - + +
219B GLN* 5.6 0.2 - - + -
220B LEU* 3.6 34.5 - - + -
228B LEU* 3.7 5.3 - - - +
96C LEU* 5.6 0.4 - - + -
100C PHE* 4.7 20.4 - - + -
104C GLU 2.9 11.7 + - - +
105C VAL* 3.1 36.8 - - + +
107C GLN* 1.3 78.8 - - - +
109C GLY* 1.3 58.2 + - - +
110C ARG 3.4 0.5 + - - -
111C ALA* 3.4 20.9 + - - +
154C ARG* 5.0 0.7 - - - -
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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