Contacts of the helix formed by residues 112 - 120 (chain K) in PDB entry 5GAG
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 GLY 112 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529A A 4.2 3.4 - - - -
558A U 3.5 3.1 - - - -
111K LYS* 1.3 74.2 - - - +
113K PRO* 1.3 77.5 - - - +
114K LEU 3.2 2.2 - - - -
115K GLY* 2.8 16.0 + - - -
116K ARG* 3.3 25.4 + - - +
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Residues in contact with PRO 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A A 3.8 16.3 + - - +
529A A 3.2 31.6 - - - +
557A C 3.9 29.2 - - - +
558A U 3.1 24.5 - - - +
112K GLY* 1.3 82.1 - - - -
114K LEU* 1.3 55.9 + - - +
116K ARG* 3.1 24.4 + - - +
117K ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A C 3.6 14.8 + - - +
558A U 2.8 27.8 + - - +
46K PRO 3.5 24.9 - - - +
47K HIS* 3.6 22.0 - - - +
48K VAL 3.9 6.7 - - - +
49K ASP* 4.1 26.5 - - + +
110K PRO* 6.1 1.6 - - + -
113K PRO* 1.3 70.6 - - - +
115K GLY* 1.3 66.8 + - - +
117K ALA* 3.3 11.2 + - + -
118K MET* 2.9 36.4 + - + +
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Residues in contact with GLY 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K LEU* 4.2 5.4 - - - +
110K PRO* 3.1 40.8 + - - +
111K LYS 5.1 0.4 - - - -
112K GLY 2.8 6.2 + - - -
114K LEU* 1.3 76.9 - - - +
116K ARG* 1.3 57.4 + - - +
118K MET* 3.0 12.2 + - - +
119K PHE* 2.9 26.6 + - - +
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Residues in contact with ARG 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A C 4.4 6.6 + - - -
528A A 2.8 61.5 + - - +
529A A 3.2 25.0 + - - -
2042A A 4.1 9.7 - - - +
112K GLY* 3.3 21.4 + - - +
113K PRO* 3.1 18.7 + - - +
115K GLY* 1.3 76.5 - - - +
117K ALA* 1.3 62.2 - - - +
119K PHE* 3.0 21.1 + - - +
120K ARG* 3.3 27.5 + - - +
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Residues in contact with ALA 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ASP* 4.7 6.6 - - + +
113K PRO 2.9 13.5 + - - +
114K LEU* 3.7 20.4 - - + +
116K ARG* 1.3 74.8 - - - +
118K MET* 1.3 61.8 + - - +
120K ARG* 3.1 32.5 + - - +
121K LYS* 4.1 9.5 + - - +
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Residues in contact with MET 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K LEU* 3.5 18.6 - - + +
37K ARG* 3.6 55.9 - - + +
44K TYR* 6.1 0.4 - - + -
46K PRO 5.4 2.0 - - - +
48K VAL 4.5 7.9 - - - +
49K ASP* 4.1 12.3 - - + +
109K LEU* 4.4 9.6 - - + -
110K PRO* 4.2 22.2 - - + -
114K LEU* 2.9 40.3 + - + +
115K GLY* 3.0 9.2 + - - +
117K ALA* 1.3 73.9 - - - +
119K PHE* 1.3 66.3 + - - +
120K ARG 3.0 2.2 - - - -
121K LYS* 2.9 31.7 + - - +
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Residues in contact with PHE 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2780A G 4.0 37.7 - + - -
36K LEU* 5.2 0.7 - - - -
102K GLU* 3.7 39.5 - - + -
105K VAL* 4.6 12.3 - - + -
106K LYS* 4.2 24.7 - - + -
109K LEU* 3.9 14.1 - - + +
115K GLY 2.9 11.8 + - - +
116K ARG* 3.0 13.4 + - - +
118K MET* 1.3 76.1 - - - +
120K ARG* 1.3 69.3 + - + +
122K LEU* 3.1 32.6 + - + +
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Residues in contact with ARG 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A C 4.8 6.6 + - - +
527A C 3.9 19.2 + - - -
528A A 5.1 5.5 + - - -
2779A U 4.0 2.4 + - - -
2780A G 2.2 43.5 + - - +
116K ARG* 3.3 14.6 + - - +
117K ALA* 3.1 47.3 + - - +
118K MET 2.9 0.4 + - - -
119K PHE* 1.3 86.1 - - + +
121K LYS* 1.3 60.1 + - + +
122K LEU 3.0 7.6 + - - +
123K LYS* 3.7 23.8 + - - +
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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