Contacts of the strand formed by residues 103 - 113 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 3.6 31.2 - - + -
97B ILE* 3.6 28.6 - - + +
98B LYS* 5.7 0.3 - - - -
100B TYR* 3.1 36.7 + - + +
101B PRO 3.2 2.5 + - - +
102B GLY* 1.3 76.9 - - - +
104B THR* 1.3 60.2 + - - +
105B SER 3.5 19.3 - - - +
106B TYR* 4.4 5.4 - - + -
125B LYS* 4.0 29.4 - - + +
126B VAL 3.5 16.8 - - - +
127B SER* 4.4 3.6 - - - +
202B 4OL 4.8 6.3 - - + -
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 6.2 0.2 - - - +
97B ILE* 4.4 11.4 - - - +
102B GLY 4.1 9.4 - - - +
103B LEU* 1.3 78.4 - - - +
105B SER* 1.3 65.1 + - - +
126B VAL* 2.9 32.4 + - - +
128B GLN 5.8 0.7 - - - +
129B ASN* 5.3 9.7 + - - +
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLY 5.0 2.5 + - - -
97B ILE* 4.2 7.0 - - - -
103B LEU* 3.5 7.3 - - - +
104B THR* 1.3 83.6 + - - +
106B TYR* 1.3 64.0 + - - +
124B LYS* 4.5 7.6 + - - -
125B LYS* 3.2 4.7 - - - -
126B VAL* 2.9 49.8 + - - +
89C PRO* 6.6 0.9 - - - -
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Residues in contact with TYR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TRP* 4.4 8.1 - + - -
81B ARG* 5.6 0.2 + - - -
83B PHE* 4.4 5.8 - + - -
93B THR* 3.4 29.2 - - - +
94B LEU* 3.6 49.3 + - + -
97B ILE* 4.1 10.4 - - + +
103B LEU* 4.4 6.3 - - + -
105B SER* 1.3 76.6 - - - +
107B LEU* 1.3 63.5 + - - +
108B VAL* 3.8 26.9 - - + -
123B PHE* 3.7 17.2 - + + -
124B LYS 3.4 4.5 - - - -
125B LYS* 3.5 28.7 - - + -
202B 4OL 3.0 49.0 + + - -
204B SO4 5.0 1.0 + - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.0 36.3 - - + -
91B GLU* 4.8 11.0 - - + +
92B PHE 3.6 14.4 - - - +
93B THR* 4.7 2.0 - - + -
106B TYR* 1.3 75.3 - - - +
108B VAL* 1.3 73.6 + - - +
109B ARG* 4.9 5.8 - - + +
122B PHE* 3.9 7.4 - - + +
123B PHE* 3.3 5.4 - - - +
124B LYS* 2.7 51.9 + - + +
87C SER* 3.8 44.9 - - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 5.3 1.6 - - + +
83B PHE* 3.8 29.8 - - + -
91B GLU* 3.2 6.8 - - - +
92B PHE* 2.8 57.1 + - + +
93B THR* 5.4 0.7 - - - -
106B TYR* 3.8 25.1 - - + -
107B LEU* 1.3 81.4 - - - +
109B ARG* 1.3 66.1 + - - +
110B VAL* 4.9 2.0 - - + +
121B VAL* 3.7 24.0 - - + -
122B PHE 3.5 2.9 - - - -
123B PHE* 3.8 12.1 - - + -
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.1 43.7 + - - +
16B VAL* 2.6 39.9 + - + +
17B PRO 3.5 24.2 - - - +
18B LEU* 3.7 23.9 - - + +
88B GLN* 4.6 8.5 - - - +
90B GLY 3.6 3.1 - - - -
91B GLU* 2.5 31.3 + - + +
107B LEU* 4.9 6.5 - - + +
108B VAL* 1.3 74.1 - - - +
110B VAL* 1.3 63.7 + - - +
111B VAL 3.3 1.0 + - - -
121B VAL* 4.0 3.6 - - - -
122B PHE* 2.8 51.5 + - + +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.7 9.0 - - - +
19B GLN* 2.9 35.0 + - + +
22B PHE* 3.8 37.5 - - + -
27B PHE* 4.4 21.5 - - + -
90B GLY* 2.9 22.5 + - - +
92B PHE* 4.3 9.2 - - + -
108B VAL* 5.2 0.9 - - + -
109B ARG* 1.3 70.3 - - - +
111B VAL* 1.3 60.0 + - - +
112B SER 4.2 4.5 - - - +
113B THR* 4.3 12.6 - - + -
120B MET 4.0 9.9 - - - +
121B VAL* 4.4 11.4 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.7 20.4 - - + -
17B PRO* 3.3 36.1 - - + +
18B LEU 3.8 2.6 - - - -
19B GLN* 3.1 17.8 + - - -
109B ARG 3.8 9.6 - - - +
110B VAL* 1.3 74.1 - - - +
112B SER* 1.3 66.2 + - - +
120B MET* 2.9 33.6 + - + +
121B VAL 4.5 1.1 - - - -
122B PHE* 3.9 10.8 - - + +
155B PHE* 4.0 26.9 - - + -
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 3.1 13.7 - - - -
110B VAL* 3.7 2.5 - - - +
111B VAL* 1.3 86.0 - - - +
113B THR* 1.3 65.3 + - - +
118B HIS* 5.3 6.3 + - - -
119B ALA* 3.2 1.4 - - - +
120B MET* 2.8 48.8 + - - +
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLN* 2.9 26.5 + - + +
22B PHE* 4.9 0.7 - - + -
27B PHE* 4.1 11.7 - - + -
31B TRP* 3.8 2.6 - - - -
110B VAL* 4.3 5.8 - - + -
112B SER* 1.3 78.3 - - - +
114B ASN* 1.3 57.4 + - - +
115B TYR* 2.9 56.0 + - + +
118B HIS* 2.7 28.8 + - - -
119B ALA* 3.4 13.6 - - - +
117D GLN* 5.1 1.4 + - - -
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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