Contacts of the strand formed by residues 106 - 111 (chain B) in PDB entry 1QY4
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 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS* 1.3 77.2 - - - +
107B GLY* 1.3 59.1 + - - -
119B TRP* 4.4 3.2 - - - -
121B SER* 3.9 3.5 - - - -
122B MET 3.0 25.4 + - - +
139B VAL 3.0 16.2 - - - -
141B ILE* 3.9 17.6 - - - +
146B PHE* 3.7 14.1 - - - -
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Residues in contact with GLY 107 (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 GLY* 1.3 75.5 - - - -
108B MET* 1.3 60.8 + - - -
119B TRP* 3.6 17.5 - - - -
120B ILE 3.1 13.2 - - - -
122B MET* 3.6 12.5 - - - +
138B THR* 3.4 4.7 - - - -
139B VAL* 2.9 29.6 + - - +
146B PHE* 3.9 3.4 - - - -
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Residues in contact with MET 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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99B TYR* 3.4 49.8 - - + -
107B GLY* 1.3 74.8 - - - -
109B LEU* 1.3 68.8 + - - +
110B LEU* 3.8 16.6 - - + +
118B LYS 3.6 1.9 - - - +
119B TRP* 3.5 8.0 - - - -
120B ILE* 2.7 39.8 + - + +
122B MET* 3.8 9.9 - - - -
128B VAL* 3.8 20.2 - - + -
130B VAL* 3.5 21.3 - - - -
136B HIS* 3.8 16.2 - - + -
137B ARG 3.3 13.5 - - - +
138B THR* 4.1 3.8 - - + -
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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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107B GLY 4.2 0.2 + - - -
108B MET* 1.3 74.4 - - - +
110B LEU* 1.3 62.6 + - - +
117B ALA* 4.6 4.3 - - + -
118B LYS 3.6 17.5 - - - +
119B TRP* 4.1 21.4 - - + -
136B HIS* 3.3 2.9 - - - -
137B ARG* 2.7 53.7 + - + +
139B VAL* 4.6 5.6 - - + -
168B PHE* 3.7 27.6 - - + -
170B LYS* 3.2 46.4 - - + +
171B ILE* 4.9 0.2 - - - -
172B VAL* 4.5 10.8 - - + -
181B VAL* 4.7 4.9 - - + -
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Residues in contact with LEU 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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5A PRO* 3.9 32.5 - - + -
108B MET* 3.8 33.7 - - + +
109B LEU* 1.3 77.6 - - - +
111B GLN* 1.3 61.9 + - - +
117B ALA* 3.2 6.4 - - - +
118B LYS* 2.8 40.4 + - + +
120B ILE* 4.0 16.2 - - + -
128B VAL* 5.3 0.2 - - + -
129B TYR 4.9 0.4 - - - +
130B VAL* 3.7 32.1 - - + -
134B TRP* 3.7 20.4 - - + -
135B ALA 3.1 7.2 - - - +
136B HIS* 4.1 3.6 - - + -
168B PHE* 4.3 2.7 - - - -
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Residues in contact with GLN 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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89B PHE* 3.6 11.6 - - + -
110B LEU* 1.3 75.6 - - - +
112B THR* 1.3 71.4 + - - +
113B PRO 5.5 1.2 + - - -
115B GLY* 4.1 12.3 - - - -
116B ASP 3.0 17.5 - - - +
117B ALA* 4.2 2.6 - - + +
134B TRP* 3.5 7.7 - - - -
135B ALA* 3.0 32.0 + - + -
162B THR* 5.8 2.0 - - - +
163B ILE* 4.2 10.9 - - - +
167B GLY 3.7 16.6 + - - -
168B PHE* 3.4 23.0 - - + +
169B SER* 2.8 35.0 + - - +
187B TRP* 4.5 6.1 - - - +
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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