Contacts of the strand formed by residues 72 - 82 (chain F) in PDB entry 5HK5
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 TRP 72 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 3.9 21.6 - - + +
100E GLN* 4.8 4.7 + - - -
70F SER 4.3 7.4 - - - -
71F ASP* 1.3 77.9 - - - +
73F CYS* 1.3 68.0 + - - +
74F LYS* 4.5 7.6 - - + -
98F TYR* 3.4 53.6 - + - -
99F GLY* 3.7 3.8 - - - -
100F GLN* 2.9 78.4 + - + +
157F CYS* 3.8 1.9 - - - -
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Residues in contact with CYS 73 (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 TRP* 1.3 79.5 - - - +
74F LYS* 1.3 60.3 + - - +
98F TYR 3.6 4.3 - - - -
123F CYS* 2.1 47.3 - - - -
155F CYS* 3.4 16.7 + - - +
156F ARG* 3.2 36.1 - - - -
157F CYS* 3.6 19.5 - - - +
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Residues in contact with LYS 74 (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 TRP* 4.5 7.7 - - + -
73F CYS* 1.3 77.2 - - - +
75F THR* 1.3 100.7 + - + +
76F GLN* 4.2 14.6 - - - +
95F ARG* 6.0 0.4 - - - +
97F CYS* 3.6 3.8 - - - -
98F TYR 3.0 34.1 + - - +
155F CYS* 3.9 5.0 - - - +
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Residues in contact with THR 75 (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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74F LYS* 1.3 113.0 + - + +
76F GLN* 1.3 64.1 + - - +
95F ARG* 2.6 50.9 + - - +
96F PHE 3.5 5.4 + - - -
152F VAL* 4.3 4.3 - - - +
153F LYS 4.1 15.9 + - - +
154F HIS* 5.4 3.1 - - + -
155F CYS* 4.0 15.7 - - - +
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Residues in contact with GLN 76 (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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63E THR* 5.3 2.4 + - - -
67E TYR* 5.3 10.3 - - - +
74F LYS* 4.2 16.4 - - - +
75F THR* 1.3 86.0 + - - +
77F PRO* 1.4 77.7 - - + +
95F ARG* 3.1 10.3 - - - +
96F PHE* 2.8 68.4 + - + +
98F TYR* 4.4 18.4 + - + -
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Residues in contact with PRO 77 (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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62E VAL 3.8 5.9 - - - +
63E THR* 5.6 0.2 - - - -
76F GLN* 1.4 94.9 - - + +
78F LEU* 1.3 59.0 + - - +
79F ARG* 5.9 1.3 - - + -
93F LEU* 4.8 16.6 - - + -
94F ASN 4.0 6.1 - - - +
95F ARG* 4.1 12.5 - - - +
96F PHE* 3.5 16.6 - - + -
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Residues in contact with LEU 78 (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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60E LEU* 4.1 15.9 - - + -
61E VAL 3.6 23.6 - - - +
62E VAL* 3.7 22.9 - - + +
106E ILE* 4.4 7.4 - - + -
107E PRO* 4.2 19.3 - - + -
110E VAL* 4.1 25.6 - - + -
76F GLN 3.5 0.2 + - - -
77F PRO* 1.3 74.3 - - - +
79F ARG* 1.3 67.8 + - - +
80F GLN* 3.5 1.5 + - + +
93F LEU* 3.7 4.2 - - - +
94F ASN* 2.8 47.5 + - + +
95F ARG 4.1 6.7 - - - +
96F PHE* 4.1 15.3 - - + -
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Residues in contact with ARG 79 (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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60E LEU* 4.0 17.0 - - - +
61E VAL 4.8 4.7 + - - +
77F PRO* 5.9 1.3 - - + -
78F LEU* 1.3 73.7 - - - +
80F GLN* 1.3 59.8 + - - +
81F THR* 4.3 0.9 + - - -
91F THR* 4.3 16.6 - - + +
92F ILE 3.7 5.4 - - - -
93F LEU* 3.8 19.6 - - + +
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Residues in contact with GLN 80 (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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60E LEU* 5.0 2.9 - - - -
108E ARG 4.1 2.6 + - - -
109E HIS 2.9 27.7 + - - -
110E VAL* 3.6 29.6 - - + +
78F LEU* 3.5 3.1 + - + +
79F ARG* 1.3 74.5 - - - +
81F THR* 1.3 70.1 + - - +
82F VAL* 4.6 1.8 - - + +
91F THR* 3.4 5.1 - - - +
92F ILE* 2.8 58.1 + - + +
94F ASN* 2.7 36.4 + - + +
149F ILE* 3.5 25.7 - - - +
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Residues in contact with THR 81 (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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60E LEU* 5.8 0.8 - - - +
109E HIS 4.3 5.2 - - - +
110E VAL 3.5 21.1 + - - +
112E LYS 5.8 0.3 + - - -
79F ARG 4.3 0.4 + - - -
80F GLN* 1.3 77.9 - - - +
82F VAL* 1.3 63.7 + - - +
83F SER* 3.5 25.3 + - - +
89F SER* 4.0 10.8 - - - +
90F ARG 3.8 4.7 - - - +
91F THR* 4.4 9.7 + - - +
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Residues in contact with VAL 82 (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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109E HIS 5.8 0.4 - - - -
80F GLN* 4.6 3.1 - - - +
81F THR* 1.3 76.2 - - - +
83F SER* 1.3 58.9 + - - +
89F SER* 3.4 2.8 - - - -
90F ARG 2.9 36.7 + - - +
92F ILE* 3.7 28.0 - - + -
133F VAL* 3.9 17.3 - - + -
135F LEU* 3.4 20.2 - - + +
147F LYS* 3.6 34.3 - - + -
149F ILE* 4.1 23.8 - - + -
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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