Contacts of the helix formed by residues 103 - 115 (chain A) in PDB entry 5HS6
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLN* 5.3 0.8 - - - +
101A GLU 5.3 0.4 - - - -
102A THR* 1.3 79.3 - - - +
104A ALA* 1.3 59.1 - - - +
105A GLN* 3.4 7.0 + - - +
106A GLY* 2.7 31.1 + - - -
107A PHE* 2.9 30.0 + - - +
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Residues in contact with ALA 104 (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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103A SER* 1.3 73.2 - - - +
105A GLN* 1.3 57.2 + - - +
107A PHE* 3.3 10.1 + - - +
108A ARG* 2.8 56.1 + - - +
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Residues in contact with GLN 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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103A SER* 3.2 6.9 + - - +
104A ALA* 1.3 77.6 - - - +
106A GLY* 1.3 58.5 + - - +
108A ARG* 2.9 37.6 + - - +
109A GLN* 3.0 51.9 + - - +
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Residues in contact with GLY 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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103A SER* 2.7 23.9 + - - -
105A GLN* 1.3 69.9 - - - +
107A PHE* 1.3 63.6 + - - +
109A GLN* 3.3 17.4 + - - +
110A LEU* 3.0 24.1 + - - +
153A PRO* 5.5 1.8 - - - -
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Residues in contact with PHE 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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102A THR* 5.9 1.6 - - - -
103A SER 2.9 14.9 + - - +
104A ALA* 3.3 13.9 - - - +
106A GLY* 1.3 75.9 - - - +
108A ARG* 1.3 63.0 + - + +
110A LEU* 3.2 2.4 + - - +
111A LEU* 2.9 46.6 + - + +
152A VAL* 4.4 13.7 - - + -
153A PRO* 3.9 44.1 - - + +
156A ALA* 3.5 28.9 - - + -
157A THR* 5.0 0.7 - - + -
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Residues in contact with ARG 108 (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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104A ALA* 2.8 50.1 + - - +
105A GLN* 2.9 38.6 + - - +
107A PHE* 1.3 72.7 - - + +
109A GLN* 1.3 58.6 + - + +
111A LEU* 3.2 16.9 + - + +
112A GLU* 2.9 32.5 + - + +
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Residues in contact with GLN 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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105A GLN* 3.0 38.1 + - + +
106A GLY* 3.7 16.9 - - - +
107A PHE 3.3 0.4 - - - -
108A ARG* 1.3 74.8 - - + +
110A LEU* 1.3 62.6 + - - +
112A GLU* 3.1 21.2 + - + +
113A LEU* 3.3 12.0 + - - +
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Residues in contact with LEU 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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92A HIS* 3.5 33.7 - - + +
94A PRO* 3.7 28.7 - - + -
106A GLY 3.0 16.2 + - - +
107A PHE* 3.2 5.8 + - - +
109A GLN* 1.3 76.0 - - - +
111A LEU* 1.3 58.0 - - - +
113A LEU* 3.3 4.3 + - + +
114A ASN* 2.9 44.5 + - - +
153A PRO* 3.7 12.3 - - + +
154A TYR* 3.5 38.6 - - + +
157A THR* 4.0 4.7 - - + -
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Residues in contact with LEU 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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107A PHE* 2.9 47.4 + - + +
108A ARG* 3.4 14.8 - - + +
110A LEU* 1.3 73.9 - - - +
112A GLU* 1.3 65.1 + - - +
115A LEU* 3.0 34.9 + - + +
116A LEU* 2.9 30.3 + - + +
156A ALA* 5.4 1.3 - - + -
157A THR* 3.7 24.0 - - + -
160A ALA* 5.4 1.3 - - + -
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Residues in contact with GLU 112 (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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64A THR* 3.8 29.9 - - + +
108A ARG* 2.9 19.6 + - + +
109A GLN* 3.1 15.0 + - + +
111A LEU* 1.3 76.4 - - - +
113A LEU* 1.3 57.6 + - - +
116A LEU* 3.1 33.7 + - - +
117A GLY* 2.9 27.0 + - - -
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Residues in contact with LEU 113 (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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63A VAL* 3.7 12.7 - - + +
64A THR* 3.7 9.9 - - + -
90A ALA 4.2 6.3 - - - +
91A GLY* 3.6 13.0 - - - +
92A HIS* 3.5 38.6 - - + +
109A GLN 3.3 9.1 + - - +
110A LEU* 4.0 6.1 - - + +
111A LEU 3.3 0.2 - - - -
112A GLU* 1.3 81.7 - - - +
114A ASN* 1.3 72.1 + - - +
115A LEU 3.4 0.7 + - - -
117A GLY* 3.8 11.6 + - - -
118A THR 4.3 2.3 + - - -
301A NAD 3.3 48.7 - - + +
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Residues in contact with ASN 114 (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 ALA 4.6 6.1 - - - +
91A GLY* 3.2 7.1 - - - -
92A HIS 2.9 43.6 + - - +
110A LEU* 2.9 26.8 + - - +
113A LEU* 1.3 78.6 - - - +
115A LEU* 1.3 57.8 + - - +
118A THR* 3.6 12.2 + - - -
154A TYR* 3.6 14.5 - - - -
157A THR* 3.0 32.2 + - - +
158A LYS* 4.2 13.0 + - + +
161A VAL* 3.3 18.5 - - - +
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Residues in contact with LEU 115 (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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111A LEU* 3.0 35.5 + - + +
113A LEU 3.3 0.2 - - - -
114A ASN* 1.3 79.7 - - - +
116A LEU* 1.3 75.7 + - + +
117A GLY 3.3 1.1 - - - -
118A THR* 3.3 5.8 + - - -
119A TYR* 3.0 25.4 + - + +
157A THR* 4.7 4.5 - - - +
160A ALA* 3.7 34.3 - - + +
161A VAL* 3.9 12.8 - - + +
164A MET* 3.8 27.8 - - + -
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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