Contacts of the helix formed by residues 107 - 115 (chain B) in PDB entry 6W6Y
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 GLN 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASP* 3.1 25.5 + - - +
106B ILE* 1.3 82.4 - - + +
108B LEU* 1.3 62.4 - - + +
109B LEU 3.0 1.3 + - - -
110B LYS* 3.2 24.4 + - - +
111B SER* 4.0 1.4 + - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.6 48.7 - - + +
78B GLY* 4.0 2.3 - - - -
98B PRO* 3.9 4.2 - - + +
104B GLU* 5.3 1.8 - - + -
105B ASP* 3.0 34.2 + - + +
107B GLN* 1.3 77.7 - - + +
109B LEU* 1.3 58.1 + - - +
110B LYS 3.2 0.4 - - - -
111B SER* 3.2 16.5 + - - +
112B ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PRO* 3.6 13.2 - - + +
106B ILE* 3.0 35.6 + - + +
108B LEU* 1.3 76.8 - - - +
110B LYS* 1.3 62.1 + - - +
112B ALA* 3.3 4.7 + - + +
113B TYR* 3.1 49.2 + - + -
127B LEU* 3.8 18.4 - - + +
128B SER* 3.8 21.5 - - - +
134B ALA* 4.6 6.1 - - + -
138B HIS* 4.3 3.1 - - + -
139B SER* 3.9 28.3 - - - +
142B VAL* 3.9 15.9 - - + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE 4.5 0.2 + - - -
107B GLN* 3.2 16.3 + - - +
109B LEU* 1.3 74.4 - - - +
111B SER* 1.3 59.7 + - - +
113B TYR 3.0 2.3 + - - -
114B GLU* 2.8 48.6 + - - +
142B VAL* 3.7 16.6 - - + +
145B ASP* 4.2 9.7 + - - +
146B THR* 3.3 37.3 + - + +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 4.9 5.9 + - - -
77B VAL 5.0 0.3 + - - -
78B GLY* 3.0 21.0 + - - +
107B GLN 4.0 1.6 + - - -
108B LEU* 3.2 23.4 + - - +
110B LYS* 1.3 77.7 - - - +
112B ALA* 1.3 64.7 + - - +
114B GLU* 3.2 29.5 + - - +
115B ASN* 3.2 10.2 + - - -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLY* 3.6 11.1 + - - -
95B VAL* 3.4 15.3 - - + +
96B VAL 3.8 20.0 - - - +
97B GLY* 4.0 9.0 - - - -
108B LEU 2.9 14.0 + - - +
109B LEU* 3.4 11.4 - - + +
111B SER* 1.3 77.2 + - - +
113B TYR* 1.3 61.9 + - - +
115B ASN* 2.9 22.3 + - - +
116B PHE* 4.2 1.7 - - - -
127B LEU* 3.8 16.6 - - + -
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.1 37.1 + - + -
110B LYS 3.0 7.4 + - - +
112B ALA* 1.3 74.2 - - - +
114B GLU* 1.3 65.2 + - - +
116B PHE* 2.9 46.0 + + - +
117B ASN* 4.2 0.7 + - - -
125B PRO 4.8 2.5 - - - -
126B LEU* 3.6 11.8 - - - +
127B LEU* 3.0 33.2 + - + -
139B SER* 2.6 46.7 + - - -
142B VAL* 3.7 12.6 - - + -
143B CYS* 3.5 27.4 - - + -
146B THR* 3.9 15.9 - - + -
147B VAL* 3.7 11.1 - - + +
153B LEU* 5.3 0.9 - - + -
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS* 2.8 42.2 + - - +
111B SER* 3.2 20.5 + - - +
113B TYR* 1.3 71.4 - - - +
115B ASN* 1.3 62.9 + - - +
117B ASN* 3.0 32.5 + - - +
118B GLN* 4.5 6.5 + - - -
146B THR* 3.6 13.6 - - + +
148B ARG* 5.6 5.1 + - - +
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Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 5.5 2.3 + - - -
78B GLY 2.9 30.3 + - - +
79B GLY* 3.8 7.6 + - - -
80B SER* 2.8 35.7 + - - +
93B LEU* 4.0 5.5 - - + +
95B VAL* 4.0 9.1 - - + +
111B SER 3.2 4.6 + - - -
112B ALA* 2.9 22.6 + - - +
113B TYR 3.1 0.8 - - - -
114B GLU* 1.3 78.8 - - - +
116B PHE* 1.3 61.7 + - - +
117B ASN 3.2 0.9 + - - -
118B GLN* 3.3 27.3 + - - +
119B HIS* 4.0 7.3 - - - -
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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