Contacts of the helix formed by residues 100 - 106 (chain C) in PDB entry 2GRA
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 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C GLY 4.0 1.4 + - - -
99C VAL* 1.3 84.9 - - - +
101C ILE* 1.3 74.1 + - + +
102C SER* 3.6 18.2 - - - +
103C SER* 3.6 26.9 - - - +
104C ILE* 3.9 8.3 + - - +
119C ARG* 3.9 6.2 - - - +
164C GLU* 3.0 17.5 - - - +
269C GLN* 3.8 23.6 + - - +
273C ASP* 4.3 9.3 + - - -
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Residues in contact with ILE 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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100C THR* 1.3 73.1 - - + +
102C SER* 1.3 80.0 + - - +
103C SER 3.0 1.6 - - - -
104C ILE* 3.0 7.8 + - + +
105C GLU* 2.8 45.4 + - - +
117C VAL* 3.3 50.9 - - + +
118C ILE* 4.1 0.4 - - - -
119C ARG* 3.8 16.8 - - + +
138C GLY* 4.3 10.5 - - - +
164C GLU* 2.7 35.8 + - + +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C THR* 4.3 9.1 - - - +
101C ILE* 1.3 90.4 - - - +
103C SER* 1.3 56.6 + - - +
105C GLU* 4.3 10.9 + - - -
106C LYS* 2.8 50.2 + - - +
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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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79C LEU* 5.6 0.2 - - - -
99C VAL* 4.8 7.4 - - - +
100C THR* 3.6 30.9 - - - -
101C ILE 3.0 0.2 - - - -
102C SER* 1.3 81.0 - - - +
104C ILE* 1.3 61.7 + - - +
106C LYS* 3.7 5.9 - - - +
107C LYS* 3.4 22.8 - - - +
272C ALA* 5.4 6.5 - - - +
273C ASP* 4.7 14.4 + - - +
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Residues in contact with ILE 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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68C LEU* 5.0 0.4 - - + -
75C ILE* 4.5 3.8 - - + -
79C LEU* 3.7 27.4 - - + -
92C VAL* 5.4 2.7 - - + -
94C SER* 4.4 23.6 - - - +
99C VAL* 4.3 18.8 - - + +
100C THR 3.9 14.1 - - - +
101C ILE* 3.0 8.3 + - + +
103C SER* 1.3 75.2 - - - +
105C GLU* 1.3 63.3 + - - +
106C LYS 3.0 5.2 + - - -
107C LYS* 3.1 2.0 + - - -
108C LEU* 2.9 52.5 + - + +
117C VAL* 4.0 28.5 - - + -
119C ARG* 6.5 0.9 - - - -
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Residues in contact with GLU 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 ILE* 2.8 42.1 + - + +
102C SER* 4.1 9.1 + - - +
104C ILE* 1.3 72.6 - - - +
106C LYS* 1.3 60.6 + - + +
107C LYS 3.4 0.4 - - - -
109C SER* 2.9 36.3 + - - +
115C PRO* 5.3 1.8 - - - -
117C VAL* 3.7 19.9 - - + +
138C GLY* 3.1 20.8 - - - +
139C THR* 2.7 42.2 + - - +
140C HIS* 4.4 8.7 + - + +
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Residues in contact with LYS 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 SER* 2.8 35.1 + - - +
103C SER* 3.7 5.1 - - - +
105C GLU* 1.3 81.0 - - + +
107C LYS* 1.3 61.2 + - - +
109C SER* 5.2 0.7 - - - -
110C ALA* 5.3 2.5 - - - +
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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