Contacts of the strand formed by residues 103 - 113 (chain C) in PDB entry 4ZHF
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 LEU 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C LEU* 3.6 30.1 - - + -
97C ILE* 3.6 28.2 - - + +
98C LYS* 5.7 0.3 - - - -
100C TYR* 3.2 37.4 + - + +
101C PRO 3.2 1.9 - - - +
102C GLY* 1.3 77.8 - - - +
104C THR* 1.3 60.3 + - - +
105C SER 3.5 19.1 - - - +
106C TYR* 4.4 5.6 - - + -
125C LYS* 4.0 29.4 - - + +
126C VAL 3.4 17.7 - - - +
127C SER* 4.4 2.9 - - - +
202C 4OL 4.7 5.8 - - + -
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Residues in contact with THR 104 (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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97C ILE* 4.4 11.7 - - - +
102C GLY 4.2 9.0 - - - +
103C LEU* 1.3 78.0 - - - +
105C SER* 1.3 64.6 + - - +
126C VAL* 3.0 32.4 + - - +
129C ASN* 5.3 8.3 + - - +
57D GLU* 5.6 5.4 - - - +
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Residues in contact with SER 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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97C ILE* 4.2 7.4 - - - -
103C LEU* 3.5 5.7 - - - +
104C THR* 1.3 82.8 + - - +
106C TYR* 1.3 65.3 + - - +
124C LYS* 4.8 7.0 + - - -
125C LYS* 3.2 5.7 - - - +
126C VAL* 2.9 51.2 + - - +
178D GLY 5.1 1.9 + - - -
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Residues in contact with TYR 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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79C TRP* 4.4 7.8 - + - -
81C ARG* 5.6 0.3 + - - -
83C PHE* 4.4 5.8 - + - -
93C THR* 3.4 29.7 - - - +
94C LEU* 3.6 49.6 + - + -
97C ILE* 4.1 10.6 - - + +
103C LEU* 4.4 6.3 - - + -
105C SER* 1.3 78.1 - - - +
107C LEU* 1.3 64.8 + - - +
108C VAL* 3.7 26.5 - - + -
123C PHE* 3.8 16.1 - + - -
124C LYS 3.4 4.5 - - - -
125C LYS* 3.5 24.0 - - + -
202C 4OL 2.9 55.4 + + - -
204C SO4 5.0 1.0 + - - -
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Residues in contact with LEU 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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87B SER* 3.8 45.8 - - - +
13C LEU* 4.0 36.6 - - + -
91C GLU* 4.8 11.0 - - + +
92C PHE 3.6 14.4 - - - +
93C THR* 4.6 2.2 - - + -
106C TYR* 1.3 74.6 - - - +
108C VAL* 1.3 73.8 + - - +
109C ARG* 4.9 5.4 - - + +
122C PHE* 3.9 7.4 - - + +
123C PHE* 3.3 5.2 - - - +
124C LYS* 2.7 52.9 + - + +
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Residues in contact with VAL 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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56C TYR* 5.4 1.3 - - + +
83C PHE* 3.8 29.8 - - + -
91C GLU* 3.2 7.7 - - - +
92C PHE* 2.8 57.6 + - + +
93C THR* 5.4 0.2 - - - -
106C TYR* 3.7 26.0 - - + -
107C LEU* 1.3 80.6 - - - +
109C ARG* 1.3 65.2 + - - +
110C VAL* 4.9 2.0 - - + +
121C VAL* 3.7 24.2 - - + -
122C PHE 3.5 2.9 - - - -
123C PHE* 3.8 13.0 - - + -
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Residues in contact with ARG 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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13C LEU* 3.1 42.1 + - - +
16C VAL* 2.6 40.0 + - + +
17C PRO 3.4 24.0 - - - +
18C LEU* 3.7 25.1 - - + +
88C GLN* 4.9 7.3 + - - -
90C GLY 3.6 3.4 - - - -
91C GLU* 2.6 31.3 + - + +
107C LEU* 5.2 5.8 - - + +
108C VAL* 1.3 74.5 - - - +
110C VAL* 1.3 63.5 + - - +
111C VAL 3.3 1.0 + - - -
121C VAL* 4.0 3.6 - - - -
122C PHE* 2.8 51.9 + - + +
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Residues in contact with VAL 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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18C LEU* 3.7 9.0 - - - +
19C GLN* 2.9 34.0 + - + +
22C PHE* 3.9 34.8 - - + -
27C PHE* 4.3 21.1 - - + -
90C GLY* 2.9 22.3 + - - +
92C PHE* 4.3 12.1 - - + -
108C VAL* 5.2 1.6 - - + -
109C ARG* 1.3 71.7 - - - +
111C VAL* 1.3 58.4 + - - +
112C SER 4.3 4.9 - - - +
113C THR* 4.3 12.1 - - + -
120C MET 4.0 9.6 - - - +
121C VAL* 4.3 10.8 - - + -
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Residues in contact with VAL 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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16C VAL* 3.7 20.6 - - + -
17C PRO* 3.3 37.2 - - + +
18C LEU 3.8 2.6 - - - -
19C GLN* 3.1 17.8 + - - -
109C ARG 3.8 9.2 - - - +
110C VAL* 1.3 72.1 - - - +
112C SER* 1.3 65.6 + - - +
120C MET* 2.9 34.9 + - + +
121C VAL 4.5 0.2 - - - -
122C PHE* 3.9 10.8 - - + +
155C PHE* 4.0 27.1 - - + -
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Residues in contact with SER 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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19C GLN* 3.1 13.7 - - - -
110C VAL* 3.7 2.1 - - - +
111C VAL* 1.3 87.1 - - - +
113C THR* 1.3 66.0 + - - +
118C HIS* 5.1 6.7 + - - -
119C ALA* 3.3 0.9 - - - +
120C MET* 2.8 49.2 + - - +
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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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117A GLN* 5.1 1.2 + - - +
19C GLN* 2.9 26.6 + - + +
22C PHE* 4.9 0.7 - - + -
27C PHE* 4.0 12.0 - - + -
31C TRP* 3.8 2.8 - - - -
110C VAL* 4.3 5.4 - - + -
112C SER* 1.3 79.2 - - - +
114C ASN* 1.3 57.5 + - - +
115C TYR* 2.9 55.5 + - + +
118C HIS* 2.7 28.8 + - - -
119C ALA* 3.4 13.9 - - - +
205C GOL 4.6 4.9 + - - -
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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