Contacts of the helix formed by residues 101 - 111 (chain B) in PDB entry 5HAN
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 MET 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A THR* 3.7 21.5 - - - +
235A ALA* 3.8 12.8 - - + -
236A ASP* 3.5 22.9 - - + +
244A ARG* 3.6 26.2 - - - +
92B ASP* 3.6 30.9 + - - +
93B ARG 4.0 6.7 - - - -
94B ASN* 3.5 23.6 - - - +
100B ALA* 1.3 75.2 - - - +
102B ILE* 1.3 65.4 + - - +
103B ALA* 4.6 3.1 - - - -
104B SER* 3.4 21.9 + - - +
105B PHE 3.7 6.4 + - - -
133B TYR* 4.0 8.2 + - - -
137B PHE* 4.0 3.8 - - - -
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Residues in contact with ILE 102 (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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236A ASP* 2.8 21.3 + - - +
101B MET* 1.3 69.8 - - - +
103B ALA* 1.4 62.4 + - - +
105B PHE* 3.2 27.3 + - + -
106B LEU* 2.9 46.2 + - + +
127B PHE* 5.6 8.5 - - + -
137B PHE* 3.8 29.6 - - + -
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Residues in contact with ALA 103 (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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234A THR* 4.2 25.4 - - + -
236A ASP* 3.0 21.9 + - - +
267A VAL* 3.8 5.0 - - + +
268A ALA* 4.3 17.9 - - + +
101B MET* 3.2 8.0 - - - -
102B ILE* 1.4 78.8 - - - +
104B SER* 1.4 52.4 + - - +
106B LEU* 3.5 9.3 + - - +
107B THR* 2.6 37.7 + - - -
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Residues in contact with SER 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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196A PRO* 5.0 5.0 + - - +
200A GLN* 4.8 1.4 + - - -
90B LEU 4.4 0.3 + - - -
91B PHE* 3.5 10.0 - - - -
92B ASP* 2.8 46.4 + - - +
101B MET* 3.4 17.6 + - - +
102B ILE 3.2 0.4 - - - -
103B ALA* 1.4 74.8 - - - +
105B PHE* 1.4 66.6 + - - +
107B THR* 3.3 6.4 + - - -
108B LEU* 3.1 32.2 + - - +
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Residues in contact with PHE 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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24B VAL* 3.9 21.5 - - + -
26B CYS* 4.2 1.3 - - - -
91B PHE* 3.8 18.7 - + - -
101B MET 3.7 2.2 + - - -
102B ILE* 3.2 34.4 + - + +
104B SER* 1.4 77.0 - - - +
106B LEU* 1.3 67.2 + - + +
108B LEU* 4.1 0.2 - - - -
109B THR* 2.7 70.4 + - + +
124B MET* 4.1 9.9 - - + -
127B PHE* 3.7 47.1 - + + -
133B TYR* 3.8 21.1 - + + +
137B PHE* 5.1 0.4 - + + -
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Residues in contact with LEU 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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267A VAL* 3.9 37.5 - - + +
102B ILE* 2.9 39.4 + - + +
103B ALA* 3.7 4.7 - - - +
105B PHE* 1.3 87.8 - - + +
107B THR* 1.3 65.0 + - - +
109B THR* 4.2 2.9 - - - -
110B ILE* 2.9 41.6 + - + -
111B GLY* 3.3 6.4 + - - -
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Residues in contact with THR 107 (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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195A GLU* 3.3 42.9 - - + +
196A PRO* 4.4 8.5 - - + -
234A THR* 5.7 0.7 - - - +
264A ASP* 3.9 20.0 + - - +
267A VAL* 3.3 17.7 - - - +
290A ALA* 4.1 5.4 - - + -
49B GLU 5.8 0.2 - - - +
50B SER* 5.8 0.2 - - - -
103B ALA 2.6 24.6 + - - -
104B SER* 3.3 7.2 + - - -
106B LEU* 1.3 77.0 - - - +
108B LEU* 1.3 61.6 + - - +
111B GLY* 3.3 20.4 - - - -
112B ASN 4.2 3.3 + - - -
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Residues in contact with LEU 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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169A LYS* 4.7 2.9 - - + -
170A LEU* 3.9 10.1 - - + -
195A GLU* 5.6 0.9 - - - +
196A PRO* 3.6 33.0 - - + -
50B SER* 3.2 54.4 + - - +
51B SER* 4.2 4.7 - - - +
86B TYR* 4.8 1.8 - - + -
90B LEU* 3.7 34.8 - - + +
91B PHE* 3.7 29.6 - - + -
104B SER* 3.1 17.9 + - - +
105B PHE 4.2 1.1 - - - +
107B THR* 1.3 79.3 - - - +
109B THR* 1.3 64.3 + - + +
110B ILE 3.6 0.3 + - - -
111B GLY 4.3 0.2 + - - -
112B ASN 5.7 0.3 + - - -
113B ASN* 3.7 2.3 + - - -
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Residues in contact with THR 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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26B CYS* 3.8 11.7 - - - -
28B TYR* 2.7 31.4 + - - -
86B TYR* 3.8 20.4 - - + -
91B PHE* 4.1 11.2 - - + -
105B PHE* 2.7 51.2 + - + +
106B LEU* 4.2 1.4 - - - -
108B LEU* 1.3 76.4 - - - +
110B ILE* 1.4 61.5 + - - +
113B ASN* 3.0 10.7 + - - -
124B MET* 3.3 23.4 - - - +
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Residues in contact with ILE 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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267A VAL* 5.1 2.7 - - + +
291A GLY* 3.5 9.5 - - - +
294A ALA* 5.8 2.7 - - + -
28B TYR* 4.0 17.3 - - + -
105B PHE* 6.0 0.2 - - + -
106B LEU* 2.9 41.2 + - + +
109B THR* 1.4 84.8 + - - +
111B GLY* 1.3 59.7 + - - +
113B ASN* 3.7 6.7 - - - +
114B GLN* 3.2 43.6 - - + +
122B ALA 4.3 2.7 - - - +
123B LYS* 4.8 0.4 - - - -
124B MET* 4.2 27.1 - - + +
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Residues in contact with GLY 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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267A VAL* 5.1 0.4 - - - -
290A ALA* 3.9 5.2 - - - -
291A GLY* 3.1 31.0 + - - -
106B LEU 3.3 5.1 + - - -
107B THR* 3.3 17.4 + - - -
108B LEU 4.3 0.4 + - - -
109B THR 3.9 0.4 - - - -
110B ILE* 1.3 75.6 - - - +
112B ASN* 1.3 66.1 + - - +
113B ASN* 3.1 4.6 + - - +
114B GLN* 3.0 16.6 + - - +
115B GLY 4.5 0.7 + - - -
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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