Contacts of the strand formed by residues 101 - 107 (chain A) in PDB entry 1QF6
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ARG* 3.5 26.4 - - - +
97A VAL* 3.5 1.2 - - - +
98A ILE* 3.0 26.4 + - - +
99A ASP 3.0 3.0 + - - -
100A ASN* 1.3 82.3 - - - +
102A PHE* 1.3 69.1 + - - +
220A GLY 3.3 10.8 - - - -
221A THR* 4.0 3.4 - - - -
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Residues in contact with PHE 102 (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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72A ARG* 3.8 21.1 - - + +
75A CYS* 4.0 20.9 - - + -
76A ALA* 3.5 30.5 - - + -
79A LEU* 4.1 22.2 - - + -
96A PRO 3.2 17.7 - - - +
97A VAL* 4.2 2.9 - - - -
98A ILE* 4.0 10.7 - - - +
101A GLY* 1.3 81.0 - - - +
103A TYR* 1.3 72.1 + - - +
104A TYR* 5.7 0.2 - - + -
124A MET* 5.4 3.4 - - - -
196A PHE* 5.1 3.8 - + + -
198A LEU* 4.2 11.7 - - + -
219A TYR* 3.6 2.9 - - - +
220A GLY* 2.9 56.5 + - - +
221A THR 3.6 14.8 - - - -
222A ALA* 4.4 3.6 - - + -
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Residues in contact with TYR 103 (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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76A ALA* 4.4 0.9 - - - +
94A ILE* 3.6 10.8 - - + +
95A GLY* 3.2 22.0 - - - -
96A PRO* 3.3 36.6 + - + +
98A ILE* 3.5 33.7 - - + -
102A PHE* 1.3 85.0 - - - +
104A TYR* 1.3 68.8 + - - +
105A ASP* 3.5 13.9 + - - -
217A ARG* 3.1 58.1 + - + -
218A ILE 3.0 15.9 - - - +
219A TYR* 3.9 12.3 - + + -
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Residues in contact with TYR 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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76A ALA* 3.4 30.5 - - + -
77A HIS* 4.8 0.7 - + - -
79A LEU* 4.3 20.2 - - + -
80A GLY 4.6 1.8 - - - -
92A MET* 3.6 31.5 - - + +
93A ALA 3.6 14.8 - - - -
94A ILE 3.5 5.2 - - - -
95A GLY* 3.6 27.5 + - - -
102A PHE* 5.7 0.2 - - + -
103A TYR* 1.3 76.3 - - - +
105A ASP* 1.3 90.3 + - - +
106A VAL* 3.7 3.2 + - + +
156A LYS* 2.8 29.3 + - - -
178A TYR* 4.1 1.6 - - - -
180A ASP* 2.9 24.7 + - - -
216A GLN 3.4 2.4 - - - +
218A ILE* 2.9 29.5 + - - +
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Residues in contact with ASP 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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93A ALA* 3.1 37.1 + - + +
94A ILE* 2.9 19.1 + - - +
103A TYR* 3.5 8.9 + - - -
104A TYR* 1.3 80.2 - - - +
106A VAL* 1.3 59.3 + - - +
204A ALA* 4.1 8.6 - - - +
205A TYR 5.1 3.6 - - - +
206A TRP* 5.9 2.0 - - + -
215A LEU* 4.3 14.1 - - + -
216A GLN 3.5 3.4 - - - -
217A ARG* 2.7 56.3 + - - +
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Residues in contact with VAL 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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79A LEU* 5.0 3.4 - - + -
83A ILE* 5.0 5.6 - - + -
90A THR* 3.1 34.1 - - + -
91A LYS 3.4 3.4 - - - -
92A MET* 3.9 22.7 - - + -
93A ALA 4.7 0.4 - - - +
104A TYR* 4.2 11.0 - - + +
105A ASP* 1.3 80.6 - - - +
107A ASP* 1.3 69.5 + - - +
108A LEU* 3.7 13.1 + - + +
112A LEU* 5.8 2.9 - - + -
215A LEU* 3.3 7.5 - - - +
216A GLN* 3.0 39.3 + - + +
218A ILE* 4.8 14.8 - - + -
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Residues in contact with ASP 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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89A HIS 4.2 1.7 - - - +
90A THR* 3.7 1.7 - - - -
91A LYS* 2.9 49.4 + - + +
106A VAL* 1.3 73.0 - - - +
108A LEU* 1.3 65.7 + - - +
109A ASP* 4.6 1.9 + - - +
155A TYR* 2.7 45.4 + - + +
213A LYS* 3.0 36.1 + - - +
215A LEU* 4.1 8.6 - - + +
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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