Contacts of the strand formed by residues 81 - 89 (chain C) in PDB entry 5HJD
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 PHE 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C TRP* 4.1 10.8 - + - -
55C LEU* 3.8 4.3 - - + -
56C HIS* 3.5 43.5 - + + -
59C PHE* 3.9 31.0 - + - -
79C ALA 3.7 11.7 - - - -
80C GLY* 1.3 79.9 - - - +
82C ILE* 1.3 75.6 + - - +
83C LEU* 3.4 27.3 + - + -
104C LEU* 3.1 54.1 + - + +
17D ARG* 3.3 12.7 - - - +
18D KCR 3.8 13.0 - - + -
19D GLN 5.6 0.9 - - - +
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU 6.0 0.2 - - - -
56C HIS* 6.1 0.2 - - - -
81C PHE* 1.3 79.3 - - - +
83C LEU* 1.3 61.3 + - - +
84C PRO* 3.3 12.8 - - + +
101C ASP* 3.9 33.2 - - + +
102C TYR 3.4 7.9 - - - +
103C ASP* 3.7 28.5 - - + +
17D ARG* 3.9 13.0 - - - +
20D LEU* 6.5 1.1 - - + -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TRP* 4.6 0.4 - - + -
34C VAL* 4.0 15.3 - - + -
53C PHE* 4.0 12.1 - - + -
54C HIS 3.6 30.3 - - - +
55C LEU* 3.8 15.0 - - + -
81C PHE* 3.4 30.0 + - + +
82C ILE* 1.3 68.6 - - - +
84C PRO* 1.3 68.8 - - - +
85C ILE* 3.3 14.9 + - + +
101C ASP 4.7 0.2 - - - -
102C TYR* 2.4 55.2 + - + +
104C LEU* 3.9 26.7 - - + -
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Residues in contact with PRO 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C HIS* 2.9 67.2 + - + +
82C ILE* 3.3 13.2 - - + +
83C LEU* 1.3 80.7 - - - +
85C ILE* 1.3 62.0 + - - +
86C GLU* 5.9 0.2 - - + -
99C ARG* 3.4 26.9 - - - +
100C PHE 3.4 8.3 - - - +
101C ASP* 4.2 5.2 - - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.1 14.6 - - + -
34C VAL* 4.5 9.4 - - + -
35C PHE 5.2 0.7 - - - +
36C VAL* 3.9 20.2 - - + -
51C VAL* 3.7 28.0 - - + -
52C VAL 3.5 5.2 - - - +
53C PHE* 4.0 20.9 - - + -
83C LEU* 3.5 22.7 - - + +
84C PRO* 1.3 74.4 - - - +
86C GLU* 1.3 65.6 + - - +
87C VAL* 4.1 4.7 + - + -
98C VAL 3.8 0.7 - - - +
99C ARG* 3.3 4.4 - - - +
100C PHE* 2.9 36.8 + - + +
102C TYR* 3.7 24.9 - - + -
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 3.5 3.1 - - - -
52C VAL* 2.8 41.0 + - + +
54C HIS* 3.2 29.4 + - + +
84C PRO* 5.4 0.4 - - + -
85C ILE* 1.3 78.3 - - - +
87C VAL* 1.3 62.7 + - - +
88C TYR* 3.2 32.5 + - + -
97C LYS* 3.7 28.1 + - + +
98C VAL 3.3 5.2 - - - +
99C ARG* 4.0 26.5 - - + -
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.3 16.4 - - + -
36C VAL* 4.5 9.4 - - + -
47C PHE* 5.3 0.2 - - + -
48C VAL* 3.8 33.9 - - + -
50C LYS 4.0 2.0 - - - -
51C VAL* 4.3 16.6 - - + -
85C ILE* 4.7 4.3 - - + -
86C GLU* 1.3 73.9 - - - +
88C TYR* 1.3 64.8 + - - +
89C PHE* 3.6 17.0 - - + -
97C LYS* 3.4 3.2 - - - -
98C VAL* 2.9 46.0 + - + -
100C PHE* 4.2 17.5 - - + -
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Residues in contact with TYR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C VAL* 3.4 7.8 - - - +
49C GLU* 2.9 31.0 + - - +
50C LYS* 2.9 54.1 + - + +
52C VAL* 3.9 14.6 - - + -
86C GLU* 3.2 43.9 + - + -
87C VAL* 1.3 75.2 - - - +
89C PHE* 1.3 61.9 + - - +
96C ARG* 3.7 18.2 - - + -
97C LYS* 3.2 30.4 + - + -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PHE* 3.1 26.5 - + - +
49C GLU* 4.2 11.2 - - - +
87C VAL* 3.6 18.4 - - + -
88C TYR* 1.3 77.8 - - - +
90C LYS* 1.3 59.5 + - - +
91C ASN* 2.9 42.5 + - - +
95C PRO* 3.6 9.2 - - + -
96C ARG* 3.3 19.1 + - - +
97C LYS* 3.6 23.8 - - - -
98C VAL* 3.5 26.9 - - + -
122C LEU* 3.9 16.8 - - + -
124C PHE* 3.7 32.5 - + - -
131C PHE* 3.9 8.3 - - + -
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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