Contacts of the strand formed by residues 111 - 117 (chain A) in PDB entry 4G17
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.6 11.7 - - + -
55A GLY 5.1 4.8 + - - -
58A ARG* 4.3 25.3 + - - -
73A LEU* 3.7 41.5 - - + -
74A GLU 3.5 4.7 - - - +
75A PRO* 3.6 37.0 - - + -
76A MET* 3.4 13.8 - - - +
108A CYS 2.7 42.8 + - - +
109A GLY* 5.4 0.2 - - - -
110A LYS* 1.3 88.7 - - + +
112A ASN* 1.3 58.1 + - - +
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Residues in contact with ASN 112 (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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73A LEU* 3.5 2.6 - - - -
74A GLU* 2.9 46.4 + - + +
75A PRO 5.0 0.2 - - - -
76A MET* 3.6 40.8 - - - +
83A LEU* 3.1 15.1 - - + +
105A PHE* 4.4 17.1 - - + -
106A GLY 3.7 3.9 - - - -
107A PRO* 4.3 7.6 - - - +
111A TYR* 1.3 74.8 - - - +
113A ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 113 (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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39A VAL* 4.1 20.0 - - + +
71A ILE* 4.2 4.3 - - + -
72A LYS 3.3 4.5 - - - +
73A LEU* 3.5 24.7 - - + -
83A LEU* 4.1 2.9 - - - -
104A TYR 3.9 0.5 - - - +
105A PHE* 3.1 7.2 - - - -
106A GLY 2.7 45.2 + - - +
108A CYS* 4.0 10.5 - - + -
112A ASN* 1.3 76.7 - - - +
114A MET* 1.3 60.1 + - - +
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Residues in contact with MET 114 (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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70A ALA 4.0 0.3 - - - +
71A ILE* 3.6 1.1 - - - -
72A LYS* 2.9 44.0 + - + +
83A LEU* 4.2 18.2 - - + +
86A GLU* 4.0 19.7 - - - +
87A TYR* 3.7 46.4 - - + -
90A TYR* 3.7 29.2 - - + -
102A VAL* 4.0 9.0 - - + -
104A TYR 3.2 9.4 - - - +
105A PHE* 4.0 7.2 - - + -
113A ALA* 1.3 74.4 - - - +
115A VAL* 1.3 65.2 + - - +
116A LEU* 4.0 18.1 + - + +
401A 0VN 5.7 0.2 - - - +
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Residues in contact with VAL 115 (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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39A VAL* 3.7 30.3 - - + -
43A PHE* 3.6 38.6 - - + -
69A VAL* 3.7 20.4 - - + -
70A ALA 3.6 3.8 - - - +
71A ILE* 4.1 13.7 - - + -
102A VAL* 3.6 5.1 - - - +
103A TYR* 2.7 35.2 + - + -
104A TYR* 2.7 29.5 + - + +
114A MET* 1.3 75.2 - - - +
116A LEU* 1.3 58.7 - - - +
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Residues in contact with LEU 116 (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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57A LEU* 5.4 0.2 - - + -
69A VAL* 3.3 6.2 - - - +
70A ALA* 2.8 53.7 + - + +
71A ILE 4.6 0.4 - - - +
72A LYS* 4.8 6.3 - - + +
90A TYR* 4.0 22.0 - - + +
100A PRO* 4.6 7.2 - - + -
101A GLN 3.2 14.8 - - - +
102A VAL* 4.4 5.6 - - + -
103A TYR* 3.7 7.4 - - - -
114A MET* 4.0 32.1 - - + +
115A VAL* 1.3 77.4 - - - +
117A GLU* 1.3 62.4 + - - +
401A 0VN 3.4 42.0 - - + +
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Residues in contact with GLU 117 (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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68A TYR 5.5 0.2 - - - -
69A VAL* 5.0 0.7 - - - +
99A ILE 4.5 1.7 - - - +
100A PRO* 3.5 10.9 - - + +
101A GLN* 2.9 43.3 + - + +
103A TYR* 3.4 24.5 - - - +
116A LEU* 1.3 72.8 - - - +
118A LEU* 1.3 72.5 + - - +
119A LEU* 3.9 16.9 - - + +
175A ASN* 5.7 3.9 - - - +
177A THR* 4.3 14.6 + - - +
182A HIS* 4.8 4.1 + - - -
401A 0VN 3.1 24.4 - - - -
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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