Contacts of the strand formed by residues 103 - 109 (chain C) in PDB entry 4QPL
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 TYR 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C ASN* 3.0 43.6 + - - +
102C GLU* 1.3 100.2 - - + +
104C ALA* 1.3 69.8 + - - +
105C TRP* 4.5 5.8 - + - -
121C SER* 5.8 0.9 - - - -
125C GLU* 3.4 39.1 + - + +
167C ARG* 3.5 44.0 - - + +
168C ASP 3.3 14.1 - - - +
169C ILE* 4.1 1.3 - - + +
170C ILE* 4.1 5.8 - - - +
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Residues in contact with ALA 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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99C GLY* 6.1 0.4 - - - -
103C TYR* 1.3 81.4 - - - +
105C TRP* 1.3 65.9 + - - +
106C TYR* 3.5 13.0 - - + -
115C GLN* 3.9 22.7 - - + +
121C SER* 4.6 4.9 - - - +
167C ARG* 3.4 4.3 - - - +
168C ASP 2.8 32.2 + - - +
170C ILE* 3.5 22.2 - - + -
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Residues in contact with TRP 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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103C TYR* 4.7 4.3 - + - -
104C ALA* 1.3 79.1 - - - +
106C TYR* 1.3 59.3 + - - +
115C GLN* 3.6 10.4 - - - +
116C TYR* 2.9 37.6 + + + +
121C SER* 3.5 31.9 + - - +
124C LEU* 3.7 28.5 - - + -
125C GLU* 2.8 28.6 + - + +
128C PHE* 3.6 41.7 - + + -
148C LEU* 4.2 17.5 - - + -
151C MET* 3.7 26.2 - - + -
165C ILE* 4.6 9.4 - - + -
166C LYS 3.4 15.7 - - - -
167C ARG* 3.7 28.6 - - + +
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Residues in contact with TYR 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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104C ALA* 3.5 27.4 - - + +
105C TRP* 1.3 72.2 - - - +
107C TYR* 1.3 61.7 + - - +
113C TRP* 3.8 26.9 - - + -
114C TRP 3.1 17.3 - - - +
115C GLN* 3.7 29.4 + - + -
116C TYR* 3.5 5.6 - - - -
165C ILE* 3.2 7.8 - - - +
166C LYS* 2.9 39.9 + - + +
168C ASP* 3.8 13.9 - - + -
169C ILE 2.8 28.3 + - - -
170C ILE* 3.4 6.6 + - - -
172C ILE* 3.7 21.2 - - + +
174C LYS* 3.0 31.0 + - + -
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Residues in contact with TYR 107 (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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106C TYR* 1.3 74.6 - - - +
108C GLU* 1.3 73.1 + - - +
113C TRP* 3.5 5.6 - - - -
114C TRP* 2.8 66.3 + + + +
115C GLN 3.7 14.4 - - - -
116C TYR* 3.7 30.5 - + + +
153C GLN* 4.1 6.5 - - + +
163C ARG* 4.0 11.7 - - + -
164C LYS 3.4 8.1 - - - +
165C ILE* 4.2 2.0 - - + -
178C ALA* 3.3 4.6 - - - -
179C GLY 3.3 15.9 + - - -
201C V3L 2.7 74.2 + + - -
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Residues in contact with GLU 108 (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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107C TYR* 1.3 75.1 - - - +
109C GLY* 1.3 69.5 + - - +
112C GLY 4.3 1.3 - - - +
113C TRP* 3.6 13.2 - - + -
114C TRP* 4.3 0.4 - - - -
161C ARG* 3.7 19.0 + - - +
162C ARG 4.1 4.5 - - - +
163C ARG* 2.9 37.2 + - + +
164C LYS* 2.8 59.5 + - + +
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Residues in contact with GLY 109 (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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107C TYR 3.5 1.8 + - - -
108C GLU* 1.3 86.0 - - - +
110C ARG* 1.3 64.6 + - - -
111C ASN 3.4 2.8 + - - -
112C GLY 2.9 20.2 + - - +
114C TRP* 3.7 12.1 - - - -
161C ARG* 4.0 8.8 + - - -
163C ARG* 4.0 0.9 - - - -
175C LYS* 4.5 0.9 - - - -
201C V3L 3.3 17.3 - - - -
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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