Contacts of the strand formed by residues 104 - 112 (chain C) in PDB entry 5J11
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 HIS 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C ARG* 4.0 0.7 - - - -
101C ASN* 2.7 63.0 + - + +
102C GLY* 3.6 0.4 - - - -
103C THR* 1.4 90.7 + - + +
105C PRO* 1.4 70.7 - - + +
106C VAL* 3.4 3.1 + - + +
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Residues in contact with PRO 105 (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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98C SER* 4.7 4.7 - - - -
99C ILE 3.6 9.6 - - - +
100C ARG* 3.9 11.4 - - + +
103C THR 3.4 9.6 - - - +
104C HIS* 1.4 81.4 - - + +
106C VAL* 1.3 61.1 + - - +
108C THR* 4.1 19.1 - - - +
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Residues in contact with VAL 106 (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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30C VAL* 3.5 24.0 - - + +
51C TYR* 3.4 43.3 - - + +
56C LEU* 4.2 8.7 - - + -
99C ILE* 2.8 14.6 + - + +
100C ARG 4.1 1.8 - - - -
101C ASN* 3.6 39.3 - - + +
104C HIS* 3.8 2.2 - - + +
105C PRO* 1.3 72.3 - - - +
107C PHE* 1.4 60.5 + - + +
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Residues in contact with PHE 107 (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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30C VAL* 4.0 37.7 - - + -
32C ILE* 3.8 27.8 - - + -
97C PHE* 3.7 23.6 - + - -
98C SER* 3.3 1.9 - - - -
99C ILE* 3.0 40.8 + - + +
105C PRO 3.7 0.4 - - - -
106C VAL* 1.4 82.0 - - - +
108C THR* 1.4 70.0 + - - +
109C ALA* 3.5 29.4 - - + -
111C ARG* 5.7 4.0 - - - -
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Residues in contact with THR 108 (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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64A ASN* 4.3 8.4 + - - -
68C TYR* 4.9 9.4 - - - +
97C PHE 3.6 12.1 - - - +
98C SER* 3.4 15.5 - - - -
105C PRO* 4.1 12.1 - - - +
107C PHE* 1.4 84.5 + - - +
109C ALA* 1.3 69.4 + - - +
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Residues in contact with ALA 109 (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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64A ASN* 3.2 15.9 - - - +
96C TYR* 3.7 0.7 - - - +
97C PHE* 3.0 48.1 + - + +
107C PHE* 3.5 25.7 - - + -
108C THR* 1.3 79.8 - - - +
110C SER* 1.3 61.7 + - - +
111C ARG* 4.2 14.4 - - - +
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Residues in contact with SER 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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64A ASN* 2.8 19.3 + - - +
65A ASN 2.8 46.5 + - - -
66A THR* 4.0 6.9 - - - +
94C ILE* 4.1 0.7 - - - -
95C LEU 3.3 9.2 - - - -
96C TYR* 3.6 25.5 - - - -
97C PHE* 5.2 0.2 - - - -
109C ALA* 1.3 75.5 - - - +
111C ARG* 1.3 74.1 + - - +
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Residues in contact with ARG 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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60A SER 5.8 0.2 - - - -
61A THR* 2.7 29.8 + - - +
62A GLU* 3.8 12.3 + - - +
63A PHE 2.9 23.4 + - - -
64A ASN* 3.3 19.1 + - - +
65A ASN* 3.6 10.8 - - - -
32C ILE* 6.0 2.8 - - - +
34C ILE* 3.9 27.3 - - + +
94C ILE* 3.8 8.2 - - - +
95C LEU* 3.0 32.2 + - + +
97C PHE* 5.2 3.8 - - + -
107C PHE* 5.7 4.0 - - - -
109C ALA* 4.2 10.9 - - - +
110C SER* 1.3 80.4 + - - +
112C TRP* 1.3 70.5 + - - +
113C MET* 3.1 1.8 + - - -
115C TYR* 5.5 2.7 - - + -
116C TYR* 3.6 27.3 + - + -
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Residues in contact with TRP 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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65A ASN* 3.5 32.8 + - + +
67A VAL 3.8 19.7 + - - -
68A SER* 3.6 19.5 - - - -
69A CYS 4.2 4.7 - - - -
143A GLN 5.5 0.4 + - - -
146A GLY* 3.9 26.7 - - - -
147A LEU* 4.8 1.6 - - + -
150A ARG* 3.7 24.0 - - + -
153A ARG* 3.4 22.0 - - - -
158A GLN* 4.5 0.2 - - - -
92C ASP* 3.5 26.7 - - - -
93C ASP* 3.7 21.5 - - - -
94C ILE* 3.6 18.2 - - + +
111C ARG* 1.3 75.3 - - - +
113C MET* 1.3 64.1 + - - +
114C VAL* 3.3 4.5 - - + +
115C TYR* 3.2 49.8 + + + +
116C TYR* 4.0 1.9 - - - -
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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