Contacts of the strand formed by residues 117 - 124 (chain F) in PDB entry 5Z62
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 117 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E TRP* 3.6 15.4 - - - -
112F ARG* 3.2 29.4 - - - -
113F CYS* 2.4 39.6 + - - -
116F CYS* 1.3 75.5 - - - +
118F ALA* 1.3 64.6 + - - +
119F HIS 3.7 1.1 - - - -
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F SER 5.6 1.3 - - - +
72F GLY* 3.4 14.4 - - - -
78F ASN* 5.5 1.3 - - - +
91F CYS* 4.9 0.9 - - - -
112F ARG* 4.1 4.8 - - - +
113F CYS* 4.1 1.7 + - + -
116F CYS* 3.5 13.9 + - - -
117F GLY* 1.3 76.3 - - - +
119F HIS* 1.3 66.9 + - - +
120F TYR* 3.4 28.7 + - + +
201F ZN 3.7 20.9 - - - -
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Residues in contact with HIS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F GLY* 2.7 13.8 + - - +
73F THR* 3.3 18.2 - - - +
74F ARG* 3.2 56.9 + - + +
77F PRO* 3.5 8.8 - - + +
78F ASN 3.1 20.1 + - - -
110F ALA* 4.6 16.4 - - + -
111F GLN 3.8 4.9 - - - -
112F ARG* 3.3 51.7 + - + -
117F GLY 3.7 0.2 - - - -
118F ALA* 1.3 71.8 + - - +
120F TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A TYR* 5.5 5.2 - + - -
512A LYS* 5.5 8.4 - - + +
77F PRO* 4.3 2.0 - - - -
78F ASN* 3.2 38.7 + - + +
80F VAL* 5.1 3.4 - - + -
89F VAL* 3.6 26.4 - - + +
91F CYS* 2.7 37.0 - - + +
103F PHE* 3.6 28.9 - + - -
105F LEU* 3.6 20.5 - - + +
110F ALA* 3.3 10.6 - - - +
111F GLN 2.9 32.1 + - - +
113F CYS* 4.5 3.8 - - + -
118F ALA* 3.4 18.6 - - + +
119F HIS* 1.3 82.1 - - - +
121F LYS* 1.3 61.8 + - - +
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Residues in contact with LYS 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F PRO* 3.9 18.2 - - + -
78F ASN 2.7 12.9 + - - +
79F LEU* 3.4 23.7 - - + -
80F VAL* 2.6 36.2 + - - +
105F LEU* 4.3 5.1 - - - +
108F GLY* 2.4 37.0 + - - +
109F GLU* 4.6 2.7 - - - +
110F ALA* 5.0 9.4 - - + +
120F TYR* 1.3 78.0 - - - +
122F LEU* 1.3 72.2 + - - +
123F VAL* 4.7 2.2 - - + -
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F VAL* 3.3 31.6 - - + +
82F SER* 3.7 19.7 - - - -
84F SER 4.1 4.3 - - - +
85F ASN* 3.4 36.1 - - - +
86F LYS* 4.0 4.7 - - - +
87F ARG* 4.5 7.4 - - + -
105F LEU* 3.7 21.0 - - + +
106F HIS 3.9 8.2 + - - +
107F LYS* 3.6 28.5 - - + +
108F GLY 5.2 2.6 + - - +
109F GLU 5.8 0.2 + - - -
121F LYS* 1.3 88.5 - - - +
123F VAL* 1.3 66.1 + - - +
124F PRO* 4.1 6.3 - - + +
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Residues in contact with VAL 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F LEU* 3.8 40.2 - - + -
80F VAL 2.8 15.5 + - - +
81F PRO* 3.3 3.7 - - + +
82F SER* 2.9 25.0 + - - -
121F LYS* 4.7 2.5 - - + -
122F LEU* 1.3 81.9 - - - +
124F PRO* 1.3 73.3 - - + +
125F GLN* 3.4 19.3 - - - +
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Residues in contact with PRO 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F SER* 3.6 8.3 - - - +
83F ILE 6.0 2.5 - - - +
84F SER 5.6 4.3 - - - +
107F LYS* 5.0 20.0 - - + -
122F LEU* 4.1 6.5 - - + +
123F VAL* 1.3 101.8 - - + +
125F GLN* 1.3 61.3 + - - +
126F GLN 4.2 0.9 + - - -
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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