Contacts of the strand formed by residues 109 - 116 (chain C) in PDB entry 2H8C
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 ARG 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C THR* 5.7 7.4 - - + -
8C LEU 4.3 2.0 - - - -
10C TRP* 3.8 4.4 - - - -
60C GLU 3.5 0.2 - - - +
61C CYS* 3.5 2.9 - - - -
62C HIS* 2.6 86.6 + - + +
105C THR* 3.1 39.3 + - + +
108C GLY* 1.3 74.3 - - - +
110C LEU* 1.3 61.6 + - - +
111C GLU* 4.8 7.4 - - + +
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Residues in contact with LEU 110 (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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6C ILE 4.1 0.2 - - - +
7C THR* 3.6 3.5 - - - +
8C LEU* 2.7 53.8 + - + +
9C PRO 3.7 17.3 - - - +
10C TRP* 4.5 6.9 - - + -
11C PRO* 3.7 25.6 - - + -
34C TYR* 4.0 6.1 - - - +
59C ILE* 3.7 26.2 - - + -
60C GLU 3.2 2.5 - - - +
61C CYS* 3.8 24.9 - - + -
74C LEU* 4.2 14.4 - - + -
78C ALA* 4.9 13.9 - - + -
109C ARG* 1.3 73.4 - - - +
111C GLU* 1.3 63.0 + - - +
112C LEU* 4.0 5.6 - - + -
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Residues in contact with GLU 111 (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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5C SER* 5.9 1.2 - - - -
6C ILE 3.4 10.6 + - - +
7C THR* 2.7 42.2 + - + +
58C ARG 3.5 3.1 - - - +
60C GLU* 2.7 61.3 + - + +
62C HIS* 3.7 21.5 - - + +
109C ARG* 4.8 7.1 - - + -
110C LEU* 1.3 72.9 - - - +
112C LEU* 1.3 67.5 + - - +
113C THR* 4.1 0.5 + - - +
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Residues in contact with LEU 112 (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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4C TYR 4.6 0.4 - - - -
5C SER* 3.4 4.5 + - - -
6C ILE* 2.6 58.1 + - + +
8C LEU* 4.6 7.4 - - + -
57C ILE* 3.3 31.2 - - + -
58C ARG 3.5 4.0 - - - +
59C ILE* 3.7 30.7 - - + -
78C ALA* 5.0 9.6 - - + -
79C PHE* 5.4 0.7 - - + -
82C LEU* 4.5 17.7 - - + -
110C LEU* 4.0 11.0 - - + +
111C GLU* 1.3 92.5 - - - +
113C THR* 1.3 63.5 - - - +
114C ILE* 4.6 6.7 - - + -
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Residues in contact with THR 113 (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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3C THR* 5.2 6.5 - - + -
4C TYR 3.6 4.3 - - - -
5C SER* 3.3 22.0 - - - +
57C ILE* 3.7 2.3 - - - +
58C ARG* 3.2 56.9 + - - +
111C GLU* 4.1 0.6 + - - +
112C LEU* 1.3 74.1 - - - +
114C ILE* 1.3 70.0 + - - +
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Residues in contact with ILE 114 (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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3C THR* 2.7 26.0 + - - -
4C TYR* 2.9 39.6 + - + +
6C ILE* 4.3 18.4 - - + -
51C LEU* 5.5 2.2 - - + -
55C VAL* 4.0 22.0 - - + -
56C LYS 3.2 15.5 - - - +
57C ILE* 3.8 21.1 - - + -
82C LEU* 4.9 1.8 - - + -
87C PHE* 3.3 46.2 - - + -
88C TRP* 5.3 0.2 - - + -
112C LEU* 4.6 6.3 - - + -
113C THR* 1.3 82.1 - - - +
115C THR* 1.3 69.0 + - - +
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Residues in contact with THR 115 (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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2C ASN 4.0 11.4 - - - +
3C THR* 2.9 26.0 - - - +
4C TYR* 4.4 1.8 - - - -
51C LEU* 5.7 0.2 - - - -
55C VAL* 3.5 1.6 - - - -
56C LYS* 3.0 49.3 + - - +
114C ILE* 1.3 83.0 - - - +
116C GLU* 1.3 61.6 + - - +
117C MET* 3.4 8.6 + - - +
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Residues in contact with GLU 116 (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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2C ASN 4.2 4.6 + - - +
4C TYR* 4.2 17.7 - - - +
51C LEU* 3.8 38.4 - - + -
53C MET* 5.0 4.0 - - + -
54C PRO 3.5 8.3 - - - +
55C VAL* 4.7 1.1 - - - +
115C THR* 1.3 70.6 - - - +
117C MET* 1.3 54.6 + - - +
118C GLY* 2.6 20.4 + - - +
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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