Contacts of the strand formed by residues 111 - 116 (chain H) in PDB entry 6A5T
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 ILE 111 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H PHE* 4.7 13.0 - - + -
104H GLU 4.0 6.1 - - - +
105H GLU* 4.4 17.5 - - + -
106H GLY 4.5 1.6 - - - +
107H ASP 4.8 3.1 - - - +
108H GLU 4.5 5.6 - - - +
109H ASP* 3.2 12.3 + - - +
110H LYS* 1.3 75.3 - - - +
112H LYS* 1.3 64.9 + - - +
113H VAL* 4.6 8.1 - - + -
125H GLU* 3.0 23.9 - - - +
126H GLY 3.5 7.6 + - - +
128H TYR* 3.2 57.4 - - + +
131H LEU* 3.4 23.5 - - + +
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Residues in contact with LYS 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LYS* 6.0 1.4 - - - +
102H LYS 4.2 0.9 - - - +
103H PHE* 4.1 0.2 - - - -
104H GLU* 3.2 39.8 + - + +
110H LYS* 3.8 14.5 + - - +
111H ILE* 1.3 74.8 - - - +
113H VAL* 1.3 61.0 + - - +
114H TYR* 3.5 36.6 + - + +
123H CYS* 4.9 1.3 - - - -
124H LEU 3.2 5.8 - - - +
125H GLU* 3.3 35.0 + - + +
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Residues in contact with VAL 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H VAL* 4.8 7.2 - - + -
102H LYS 3.6 8.1 - - - +
103H PHE* 3.4 37.9 - - + -
111H ILE* 4.6 9.4 - - + -
112H LYS* 1.3 75.3 - - - +
114H TYR* 1.3 66.2 + - - +
115H VAL* 4.0 22.9 - - + -
122H MET* 3.0 6.1 - - + +
124H LEU* 2.6 47.3 + - + +
131H LEU* 4.9 4.5 - - + -
134H LEU* 4.7 21.3 - - + -
139H LEU* 5.5 0.4 - - + -
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Residues in contact with TYR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A SER* 6.1 0.3 - - - -
598A LEU* 3.7 42.1 + - + +
599A LEU* 5.0 8.9 + - + +
101H TYR* 2.9 47.6 + - + -
102H LYS* 3.0 48.5 + - + +
104H GLU* 4.6 5.4 + - - -
112H LYS* 3.5 34.0 + - + +
113H VAL* 1.3 78.1 - - - +
115H VAL* 1.3 62.0 + - - +
122H MET 3.3 9.6 - - - +
123H CYS* 4.2 25.6 - - + -
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Residues in contact with VAL 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H GLY 4.0 1.6 - - - -
99H THR 3.1 26.7 - - - +
100H VAL* 3.5 19.5 - - + +
101H TYR* 4.1 2.1 - - - -
113H VAL* 4.0 11.6 - - + -
114H TYR* 1.3 76.5 - - - +
116H SER* 1.3 57.7 - - - +
117H PHE* 3.7 25.4 + - + -
121H LEU* 3.1 3.5 - - - +
122H MET* 2.7 49.3 + - + +
139H LEU* 3.5 31.0 - - + -
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Residues in contact with SER 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A MET* 2.6 46.0 + - - +
98H GLY* 3.3 1.4 - - - -
99H THR* 2.9 31.8 + - - -
101H TYR* 3.8 16.7 - - - -
115H VAL* 1.3 73.8 - - - +
117H PHE* 1.3 59.4 + - - +
118H GLY* 3.4 4.7 + - - -
119H GLY 3.7 6.6 + - - -
120H LEU 3.0 10.2 + - - -
121H LEU* 3.6 10.5 - - - +
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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