Contacts of the helix formed by residues 102 - 111 (chain K) in PDB entry 6V01
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 102 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K TYR* 3.2 10.1 + - - -
101K ILE* 1.3 77.9 - - - +
103K ALA* 1.3 59.3 + - - +
104K ALA* 3.6 8.5 + - - +
105K GLU* 3.0 26.9 + - - +
106K LEU* 2.8 28.1 + - - +
135K GLY* 3.4 26.5 - - - -
137K VAL* 4.9 0.9 - - - -
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Residues in contact with ALA 103 (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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102K SER* 1.3 74.1 - - - +
104K ALA* 1.3 57.7 + - - +
106K LEU* 4.0 5.0 - - - +
107K ARG* 2.9 38.2 + - + +
126K ILE* 5.1 14.0 - - + +
130K ASP* 5.3 9.9 - - + -
134K ASP 5.0 7.3 + - - +
135K GLY* 4.7 5.4 - - - -
137K VAL* 5.3 3.9 - - + +
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Residues in contact with ALA 104 (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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102K SER* 3.2 7.4 + - - +
103K ALA* 1.3 79.9 - - - +
105K GLU* 1.3 58.9 + - - +
107K ARG* 3.4 6.5 + - - +
108K HIS* 2.9 27.9 + - - +
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Residues in contact with GLU 105 (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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100K TYR* 4.4 17.5 - - + +
101K ILE* 4.4 7.6 - - + -
102K SER* 3.0 27.7 + - - +
104K ALA* 1.3 74.5 - - - +
106K LEU* 1.3 61.3 + - - +
108K HIS* 3.2 9.6 + - - +
109K VAL* 2.9 29.7 + - - +
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Residues in contact with LEU 106 (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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375J ILE* 5.0 16.4 - - + -
376J GLN* 6.0 0.9 - - - +
90K PHE* 5.4 9.0 - - + -
93K PHE* 5.9 1.8 - - + -
101K ILE* 4.0 20.3 - - + +
102K SER 2.8 18.6 + - - +
103K ALA* 4.0 4.9 - - - +
105K GLU* 1.3 75.1 - - - +
107K ARG* 1.3 58.9 + - - +
109K VAL* 3.4 18.4 - - + +
110K MET* 2.9 35.5 + - + +
126K ILE* 4.2 22.0 - - + -
129K ALA* 5.7 2.2 - - + -
137K VAL* 4.0 25.8 - - + +
142K PHE* 5.8 8.3 - - + -
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Residues in contact with ARG 107 (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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103K ALA* 2.9 24.5 + - + +
104K ALA* 3.7 7.0 - - - +
106K LEU* 1.3 76.2 - - + +
108K HIS* 1.3 63.4 + - - +
110K MET* 4.2 5.2 - - - -
111K THR* 3.3 46.3 + - + +
119K ASP* 4.9 12.5 + - - +
122K VAL* 4.4 12.8 + - + +
123K ASP* 4.3 30.5 - - - +
126K ILE* 5.8 5.6 - - + -
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Residues in contact with HIS 108 (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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104K ALA 2.9 17.7 + - - +
105K GLU* 3.4 10.7 - - - +
107K ARG* 1.3 78.3 - - - +
109K VAL* 1.3 58.4 + - - +
111K THR* 4.9 0.2 - - - -
112K ASN* 2.5 56.1 + - - +
113K LEU* 5.6 0.2 - - - +
92L TYR* 5.5 13.1 - - + +
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Residues in contact with VAL 109 (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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372J ALA* 5.1 3.0 - - + +
375J ILE* 6.3 0.7 - - + -
376J GLN* 4.3 8.2 + - - +
93K PHE* 3.7 48.2 - - + -
101K ILE* 5.7 2.0 - - + -
105K GLU 2.9 15.9 + - - +
106K LEU* 3.4 28.5 - - + +
108K HIS* 1.3 75.7 - - - +
110K MET* 1.3 66.1 + - - +
112K ASN 4.3 0.9 - - - -
113K LEU* 3.8 37.8 + - + +
92L TYR 5.9 2.2 - - - +
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Residues in contact with MET 110 (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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376J GLN* 2.3 44.8 + - - +
106K LEU* 2.9 23.3 + - + +
107K ARG* 4.0 6.7 - - - +
108K HIS 3.3 0.6 - - - -
109K VAL* 1.3 80.8 - - + +
111K THR* 1.3 59.7 + - - +
112K ASN 3.3 1.8 + - - -
113K LEU 4.8 0.3 - - - +
116K LYS* 4.2 2.4 - - - +
117K LEU* 4.0 10.1 + - + +
122K VAL* 4.2 21.5 - - + +
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Residues in contact with THR 111 (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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107K ARG* 3.3 37.8 + - - +
108K HIS* 4.9 0.5 - - - -
110K MET* 1.3 78.1 - - + +
112K ASN* 1.3 70.1 + - - +
116K LYS* 3.5 19.1 - - - +
117K LEU 5.3 6.5 - - - +
118K THR 6.2 0.2 - - - -
119K ASP* 5.9 4.5 - - + -
122K VAL* 4.2 20.4 - - + -
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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