Contacts of the strand formed by residues 103 - 109 (chain A) in PDB entry 2Y7Q
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 LEU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A SER* 4.3 1.6 - - - -
94A ALA 3.6 28.9 - - - +
97A VAL* 4.3 21.3 - - + -
102A PRO* 1.3 74.7 - - - +
104A PHE* 1.3 65.7 + - - +
105A LEU* 4.3 24.2 - - + -
137A SER* 3.7 1.2 - - - -
138A ILE* 3.0 58.0 + - + +
141A ALA* 4.6 10.1 - - + -
145A ASP* 5.0 15.7 - - + -
149A TYR* 5.1 5.2 - - - +
167A ILE* 4.1 22.2 - - + -
169A VAL* 5.5 0.2 - - + -
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO* 6.0 4.9 - - + -
13A TRP* 3.7 19.9 - + + -
92A ALA 3.7 0.7 - - - -
93A SER* 2.8 53.0 + - - -
102A PRO* 3.7 27.6 - - + -
103A LEU* 1.3 75.1 - - - +
105A LEU* 1.3 66.9 + - - +
136A ILE 3.5 4.9 - - - +
137A SER* 3.8 27.1 - - - -
138A ILE 5.6 1.8 - - - -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 5.1 0.2 - - - -
90A LEU* 4.8 5.2 - - + -
91A GLN 4.0 2.2 - - - +
92A ALA* 3.7 15.5 - - + -
103A LEU* 4.2 16.6 - - + -
104A PHE* 1.3 88.0 - - - +
106A ARG* 1.3 63.5 + - - +
120A TYR* 4.4 7.2 - - + -
135A ALA* 3.5 4.7 - - - -
136A ILE* 2.9 61.4 + - + +
149A TYR* 3.5 41.7 - - + -
167A ILE* 3.7 28.0 - - + -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 5.3 2.0 - - - +
13A TRP* 2.9 57.3 - - + +
90A LEU* 3.6 4.3 - - - +
91A GLN* 2.8 60.7 + - + +
105A LEU* 1.3 78.3 - - - +
107A CYS* 1.3 64.0 + - - +
108A HIS* 3.3 33.0 + - - +
120A TYR* 3.5 4.8 + - - -
133A ASN* 6.1 0.2 - - - +
135A ALA* 4.9 3.8 - - - +
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Residues in contact with CYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.6 24.2 - - - -
89A LEU 4.1 0.9 - - - -
90A LEU* 4.6 0.7 - - - -
106A ARG* 1.3 71.4 - - - +
108A HIS* 1.3 61.1 + - - +
109A GLY 4.0 0.3 + - - -
115A VAL* 4.8 3.0 - - - +
118A VAL* 4.0 22.2 - - + -
120A TYR* 2.7 26.7 + - + +
133A ASN* 2.9 24.5 - - - +
134A HIS 4.5 0.4 + - - -
151A CYS* 2.0 47.1 - - + -
152A THR 4.8 0.2 - - - -
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Residues in contact with HIS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.8 16.5 - + - -
20A GLU* 2.5 28.6 + - - -
88A LEU* 3.2 5.8 - - - +
89A LEU* 2.7 50.5 + - + +
91A GLN* 3.1 42.6 + - + +
106A ARG* 3.4 30.5 + - - +
107A CYS* 1.3 73.7 - - - +
109A GLY* 1.3 78.8 + - - +
111A ARG 4.5 8.1 - - - -
115A VAL* 4.6 1.6 - - - -
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Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.6 4.0 - - - -
87A TRP 3.2 7.9 - - - -
107A CYS 4.0 0.6 + - - -
108A HIS* 1.3 89.6 + - - +
110A TRP* 1.3 68.9 + - - -
111A ARG 3.0 13.3 + - - +
113A TRP* 4.5 7.5 - - - +
115A VAL* 3.6 25.1 - - - +
133A ASN* 5.5 0.4 + - - -
155A VAL* 5.8 0.2 - - - -
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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