Contacts of the strand formed by residues 107 - 114 (chain C) in PDB entry 6MOL
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 PRO 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR* 3.3 38.4 - - + +
71A THR* 3.5 20.9 - - - +
100A ASP* 3.3 24.9 - - - +
101A LEU* 4.1 6.5 - - + -
102A ASN* 2.8 31.7 + - - +
112A ARG* 5.9 1.0 + - - -
100C VAL 4.5 2.5 - - - +
102C ALA* 5.8 0.2 - - - -
106C ALA* 1.3 82.4 - - + +
108C ARG* 1.3 61.2 + - - +
109C TYR 5.5 0.7 - - - +
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Residues in contact with ARG 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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102A ASN* 6.2 0.4 - - - +
112A ARG* 4.0 37.8 + - - +
24C GLU* 4.5 6.1 + - - +
40C TRP* 3.7 8.4 - - - +
42C GLU* 3.5 31.4 + - - +
53C TYR* 3.6 34.3 - - + -
100C VAL* 3.1 28.6 + - + +
101C THR* 4.7 0.4 - - - +
102C ALA* 4.9 1.6 - - + +
106C ALA 3.5 3.1 + - - +
107C PRO* 1.3 75.8 + - - +
109C TYR* 1.3 124.4 + - + +
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Residues in contact with TYR 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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79A THR* 6.3 1.6 - - + -
112A ARG* 6.0 0.2 - - - -
113A MET* 4.8 10.5 - - + -
24C GLU* 3.0 29.3 + - - -
25C GLU* 3.9 3.2 + - + -
26C LEU* 3.6 44.2 - - + -
40C TRP* 3.6 31.6 - + + +
41C GLU 5.1 1.6 + - - -
98C LEU 5.3 0.2 - - - -
99C ARG* 3.5 6.0 - - - +
100C VAL* 3.0 45.6 + - + +
107C PRO* 5.5 1.2 - - - +
108C ARG* 1.3 136.3 + - + +
110C HIS* 1.3 64.0 + - - +
111C ARG* 5.7 2.7 - - - -
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Residues in contact with HIS 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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38A ALA* 5.3 2.2 - - - +
43A LEU* 4.7 9.1 - - + +
46A LEU* 3.3 26.1 - - + +
67A ASP* 5.2 1.3 - - - -
71A THR* 6.3 2.7 - - + -
76A LEU* 4.3 17.6 - - + +
80A MET* 3.3 26.1 - - - +
97C GLU* 3.1 32.8 + - + -
98C LEU 3.4 9.1 + - - -
99C ARG* 2.9 53.6 + - + -
109C TYR* 1.3 77.0 - - - +
111C ARG* 1.3 63.9 + - - +
112C VAL* 4.9 0.2 - - + -
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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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46A LEU* 3.9 5.6 - - + -
80A MET* 4.0 20.9 - - + -
25C GLU* 4.2 17.9 + - - -
26C LEU* 3.5 52.4 + - + +
27C LEU* 5.6 1.0 - - - +
28C CYS* 4.2 24.7 - - - +
96C LEU 3.7 1.0 - - - +
97C GLU* 4.4 0.2 - - - +
98C LEU* 2.8 40.8 + - + +
109C TYR* 5.7 2.5 - - + -
110C HIS* 1.3 81.7 + - - +
112C VAL* 1.3 63.3 + - - +
113C ILE* 3.4 35.1 - - + +
118C VAL* 5.3 7.3 - - - +
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Residues in contact with VAL 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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13A ARG* 3.8 38.6 - - + +
43A LEU* 4.8 6.1 - - + +
46A LEU* 3.3 28.5 - - + +
47A ILE* 4.2 13.9 - - + +
95C PRO* 4.2 14.6 - - + -
96C LEU 3.3 8.3 - - - +
97C GLU* 3.7 27.1 - - + -
111C ARG* 1.3 76.6 - - - +
113C ILE* 1.3 65.2 + - - +
114C HIS* 5.2 7.0 - - + +
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Residues in contact with ILE 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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28C CYS* 4.6 9.4 - - + -
36C LEU* 4.4 15.0 - - + -
94C VAL 3.9 0.2 - - - +
95C PRO 4.0 0.3 - - - -
96C LEU* 3.0 42.8 + - + +
98C LEU* 4.1 20.2 - - + -
111C ARG* 3.4 42.8 - - + +
112C VAL* 1.3 78.6 - - - +
114C HIS* 1.3 78.0 + - - +
115C ILE 4.3 2.0 - - - +
118C VAL* 4.1 25.1 - - + -
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Residues in contact with HIS 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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13A ARG 5.3 2.8 + - - -
14A ALA 5.2 7.3 + - - -
93C PHE* 4.3 3.9 - - - -
94C VAL* 3.5 21.2 + - - +
95C PRO* 3.6 36.7 - - + +
112C VAL* 5.2 6.2 - - + +
113C ILE* 1.3 82.2 - - - +
115C ILE* 1.3 67.4 + - - +
116C ASN* 3.4 15.2 + - - +
117C GLU* 2.9 46.3 + - + +
118C VAL* 3.6 9.0 - - - +
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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