Contacts of the strand formed by residues 107 - 113 (chain H) in PDB entry 5FHX
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 SER 107 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101H GLU* 3.3 5.0 - - - +
102H TYR* 3.0 41.4 + - - +
106H ASP* 1.3 84.5 + - - +
108H PHE* 1.3 61.9 + - - +
109H TYR* 3.7 14.1 + - - -
150L TRP* 4.6 0.7 - - - -
167L TYR* 3.9 26.1 + - - -
168L LYS* 3.9 13.5 - - - -
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Residues in contact with PHE 108 (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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70A ALA* 4.1 9.9 - - + -
71A GLN* 3.7 25.8 - - + -
74A HIS* 5.3 2.2 - + - -
99H LEU* 3.8 23.2 - - + +
100H LYS 3.2 10.3 - - - +
101H GLU* 4.2 1.1 - - + -
105H TYR* 3.6 49.1 - + + -
107H SER* 1.3 74.1 - - - +
109H TYR* 1.3 66.1 + - - +
150L TRP* 3.5 34.4 - + - -
167L TYR* 5.6 0.3 - - - +
168L LYS* 5.8 0.8 - - - +
209L ALA* 3.5 46.9 - - + +
214L PHE* 4.4 4.5 - + - -
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Residues in contact with TYR 109 (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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99H LEU* 3.5 13.0 - - - +
100H LYS* 3.0 38.4 + - + +
102H TYR* 3.7 25.0 - + - -
107H SER* 3.7 21.3 + - - -
108H PHE* 1.3 82.4 - - - +
110H PHE* 1.3 58.7 + - - +
111H ASP* 3.0 27.5 + - + -
152L SER* 4.1 7.0 - - - +
164L LEU* 3.4 23.1 - - + -
167L TYR* 3.6 53.8 + + + -
173L HIS* 3.9 17.7 + + - -
207L GLN* 5.9 3.1 - - - +
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Residues in contact with PHE 110 (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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35H HIS* 3.4 43.5 - + + -
37H ILE* 4.3 5.2 - - + -
47H TRP* 4.2 5.2 - + - -
97H THR* 3.5 23.3 - - + +
98H ARG 3.6 4.9 - - - -
99H LEU* 3.8 21.3 - - + -
109H TYR* 1.3 68.7 - - - +
111H ASP* 1.3 60.1 + - - +
112H VAL 3.6 2.0 - - - -
113H TRP* 2.8 36.1 + + + +
154L PHE* 3.8 17.8 - + + -
164L LEU* 3.8 8.5 - - - +
207L GLN* 3.5 26.4 + - - -
214L PHE* 3.4 33.0 - + - -
216L PHE* 4.2 12.6 - + - -
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Residues in contact with ASP 111 (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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98H ARG* 2.8 50.1 + - - +
100H LYS* 3.3 22.5 - - - +
109H TYR* 3.0 21.4 + - + -
110H PHE* 1.3 73.3 - - - +
112H VAL* 1.4 78.4 + - + +
113H TRP* 4.0 4.9 - - - -
163L LYS* 6.0 0.3 - - - -
164L LEU* 4.3 13.0 + - - +
173L HIS* 3.8 32.0 + - + +
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Residues in contact with VAL 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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2H VAL* 3.7 44.9 - - + +
3H GLN* 4.6 4.5 - - - -
4H LEU* 3.7 18.7 - - + +
97H THR* 2.7 23.0 + - - -
98H ARG* 3.2 20.4 + - + +
111H ASP* 1.4 99.9 + - - +
113H TRP* 1.4 64.0 + - - +
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Residues in contact with TRP 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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4H LEU* 4.2 8.9 + - - +
37H ILE* 3.9 30.5 - - + -
45H LEU* 4.7 1.6 - - + -
95H TYR* 3.8 32.1 - + + -
96H CYS 3.7 3.8 - - - -
97H THR* 3.6 12.9 + - - -
110H PHE* 2.8 44.0 + + + -
111H ASP 4.0 5.6 - - - -
112H VAL* 1.4 82.8 - - - +
114H GLY* 1.3 66.1 + - - +
154L PHE* 3.9 21.0 - + - -
161L ILE* 3.9 23.6 - - + +
162L PRO* 3.5 50.7 + - + +
163L LYS* 5.2 1.8 - - - -
164L LEU 5.0 0.4 - - - +
216L PHE* 4.4 13.7 - + - -
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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