Contacts of the helix formed by residues 101 - 111 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ASP* 3.6 45.6 + - - +
93A ARG 4.0 12.3 - - - +
94A ASN* 3.5 24.0 - - - +
100A ALA* 1.3 75.5 - - - +
102A ILE* 1.3 63.4 + - - +
103A ALA* 4.3 12.6 - - + +
104A SER* 3.4 22.9 + - - +
105A PHE 3.6 6.6 + - - -
133A TYR* 4.0 7.8 + - - -
137A PHE* 4.0 2.9 - - - -
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A MET* 1.3 69.9 - - - +
103A ALA* 1.3 67.8 + - - +
105A PHE* 3.2 16.7 + - + -
106A LEU* 2.9 27.5 + - + +
127A PHE* 5.6 0.4 - - + -
137A PHE* 3.8 27.3 - - + -
270A PRO* 3.5 33.9 - - + -
312A MET* 4.0 46.7 - - + +
315A LEU* 4.3 12.8 - - + -
316A GLN* 3.8 22.0 - - + +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A MET* 3.2 14.2 - - + +
102A ILE* 1.3 81.8 - - + +
104A SER* 1.3 52.3 + - - +
106A LEU* 3.5 10.3 + - - +
107A THR* 2.6 38.1 + - - +
270A PRO* 5.0 9.4 - - + +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 4.5 0.3 + - - -
91A PHE* 3.5 9.9 - - - -
92A ASP* 2.8 46.3 + - - +
101A MET* 3.4 18.6 + - - +
102A ILE 3.2 0.8 - - - -
103A ALA* 1.3 74.5 - - - +
105A PHE* 1.3 66.7 + - - +
107A THR* 3.3 6.3 + - - -
108A LEU* 3.1 33.1 + - - +
196B PRO* 5.0 5.2 + - - +
200B GLN* 4.9 1.0 + - - -
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.9 21.8 - - + -
26A CYS* 4.2 1.8 - - - -
91A PHE* 3.8 18.0 - + - -
101A MET 3.6 2.4 + - - -
102A ILE* 3.2 25.0 + - + +
104A SER* 1.3 77.9 - - - +
106A LEU* 1.3 57.4 + - + +
108A LEU* 4.1 0.2 - - - -
109A THR* 2.8 68.0 + - + +
110A ILE* 6.0 0.4 - - + -
124A MET* 4.1 10.5 - - + -
127A PHE* 3.7 35.9 - + + -
133A TYR* 3.8 21.3 + + + +
137A PHE* 5.6 0.2 - + - -
308A VAL* 5.3 0.2 - - + -
312A MET* 3.7 35.4 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 2.9 26.4 + - + +
103A ALA* 3.7 6.1 - - - +
105A PHE* 1.3 75.7 - - + +
107A THR* 1.3 65.7 + - - +
109A THR* 4.2 3.1 - - - -
110A ILE* 3.0 42.4 + - + -
111A GLY* 3.2 6.9 + - - -
270A PRO* 4.2 25.4 - - + -
304A TYR* 4.1 12.3 - - + +
312A MET* 3.5 36.8 - - + -
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU 5.8 0.2 - - - +
103A ALA* 2.6 25.4 + - - +
104A SER* 3.3 7.9 + - - -
106A LEU* 1.3 74.7 - - - +
108A LEU* 1.3 61.9 + - - +
111A GLY* 3.3 22.8 - - - -
112A ASN 4.1 3.3 + - - -
195B GLU* 3.4 47.7 + - + +
196B PRO* 4.4 9.6 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER* 3.2 54.0 + - - +
51A SER* 4.2 4.7 - - - +
86A TYR* 4.8 1.6 - - + -
90A LEU* 3.7 34.1 - - + +
91A PHE* 3.7 29.6 - - + -
104A SER* 3.1 18.4 + - - +
105A PHE 4.2 1.1 - - - +
107A THR* 1.3 79.7 - - - +
109A THR* 1.3 63.6 + - + +
111A GLY 4.3 0.2 + - - -
112A ASN 5.7 0.3 + - - -
113A ASN* 3.6 2.4 + - - -
169B LYS* 4.5 2.2 - - + -
170B LEU* 3.9 9.9 - - + -
195B GLU* 5.7 0.4 - - - +
196B PRO* 3.6 33.7 - - + -
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 3.8 11.7 - - - -
28A TYR* 2.7 32.0 + - - -
86A TYR* 3.8 20.6 - - + -
91A PHE* 4.1 11.9 - - + -
105A PHE* 2.8 51.4 + - + +
106A LEU* 4.2 1.2 - - - -
108A LEU* 1.3 77.0 - - - +
110A ILE* 1.3 61.8 + - - +
113A ASN* 3.1 10.4 + - - -
124A MET* 3.3 23.0 - - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 4.0 16.8 - - + -
105A PHE* 6.0 0.2 - - + -
106A LEU* 3.0 41.3 + - + +
109A THR* 1.3 84.6 - - - +
111A GLY* 1.3 64.1 + - - +
113A ASN* 3.7 7.4 - - - +
114A GLN* 3.2 37.5 - - + +
122A ALA 4.5 0.4 - - - +
124A MET* 4.2 11.9 - - + +
303A GLY* 3.2 35.0 - - - +
304A TYR* 3.9 15.5 - - + -
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU 3.2 5.3 + - - -
107A THR* 3.3 20.6 + - - -
109A THR 3.8 0.6 - - - -
110A ILE* 1.3 76.4 - - - +
112A ASN* 1.3 63.6 + - - +
113A ASN* 3.1 5.2 + - - +
114A GLN* 3.0 26.5 + - - +
115A GLY 4.4 0.9 + - - -
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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