Contacts of the helix formed by residues 98 - 117 (chain A) in PDB entry 6S6A
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 GLU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS* 3.9 24.5 + - - +
96A SER* 3.1 6.5 + - - -
97A ARG* 1.3 77.3 - - + +
99A LEU* 1.3 52.0 + - - +
100A GLU 3.3 2.7 - - - -
101A LYS* 3.1 47.1 + - + +
102A ASP* 2.8 31.1 + - - +
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Residues in contact with LEU 99 (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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93A ASP 5.1 0.4 - - - +
96A SER* 3.9 19.7 - - - +
97A ARG 3.0 11.9 + - - +
98A GLU* 1.3 73.7 - - - +
100A GLU* 1.3 57.9 + - - +
102A ASP* 3.0 15.7 + - + +
103A MET* 2.8 34.7 + - + +
144A ARG* 4.0 39.5 - - - +
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU 3.3 0.6 - - - -
99A LEU* 1.3 77.9 - - - +
101A LYS* 1.3 60.2 + - - +
103A MET* 3.7 14.4 - - - +
104A HIS* 3.3 43.1 + - + -
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Residues in contact with LYS 101 (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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67A ASP* 3.0 38.7 + - - -
98A GLU* 3.1 48.1 + - + +
100A GLU* 1.3 76.1 - - - +
102A ASP* 1.3 65.4 + - - +
104A HIS* 3.3 8.2 + - + +
105A TYR* 3.2 49.5 + - + -
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Residues in contact with ASP 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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15A LYS* 2.9 40.3 + - + +
90A TYR* 4.1 4.2 + - + -
92A PHE* 4.4 23.6 - - + -
93A ASP 4.8 2.5 + - - +
96A SER* 2.5 31.0 + - - -
98A GLU* 2.8 17.9 + - - +
99A LEU* 3.0 14.0 + - + +
101A LYS* 1.3 76.6 - - - +
103A MET* 1.3 55.8 + - + +
105A TYR* 3.2 9.1 + - - +
106A TYR* 3.0 26.9 + - - +
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Residues in contact with MET 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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92A PHE* 4.4 10.8 - - + -
99A LEU* 2.8 20.4 + - + +
100A GLU* 3.7 18.8 - - - +
101A LYS 3.3 0.2 - - - -
102A ASP* 1.3 70.5 - - + +
104A HIS* 1.3 65.5 + - + +
106A TYR* 3.3 17.6 + - - +
107A GLN* 2.8 36.4 + - - +
147A ASP* 5.4 2.5 - - + -
148A LEU* 3.7 31.0 - - + +
151A LEU* 3.5 39.0 - - + -
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Residues in contact with HIS 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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100A GLU* 3.3 34.4 + - + +
101A LYS* 3.3 10.9 + - + +
103A MET* 1.3 78.0 - - + +
105A TYR* 1.3 57.1 + - + +
107A GLN* 3.4 18.8 + - - +
108A SER* 2.7 39.2 + - - +
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Residues in contact with TYR 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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15A LYS* 6.3 4.0 - - + -
67A ASP* 3.5 30.0 + - - +
70A MET* 3.7 37.0 - - + -
71A GLU* 4.2 15.7 + - - +
74A PHE* 3.7 24.2 - + - -
90A TYR* 3.4 15.7 - - - +
101A LYS* 3.2 53.2 + - + +
102A ASP* 3.7 7.0 - - - +
104A HIS* 1.3 75.5 - - + +
106A TYR* 1.3 64.7 + - - +
108A SER* 3.4 5.6 + - - -
109A CYS* 3.1 26.7 + - - -
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Residues in contact with TYR 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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88A LEU* 5.4 2.5 - - + -
90A TYR* 3.3 41.7 + + + -
92A PHE* 3.8 14.8 - + + -
102A ASP 3.0 13.5 + - - +
103A MET* 3.3 18.1 + - - +
105A TYR* 1.3 75.5 - - - +
107A GLN* 1.3 62.4 + - + +
109A CYS* 3.1 7.2 + - + +
110A LEU* 3.0 54.4 + - + +
122A ILE* 3.6 15.8 - - + +
124A CYS* 3.1 33.5 - - - -
148A LEU* 3.8 17.0 - - + -
151A LEU 4.6 4.0 - - - -
152A SER* 2.7 24.1 + - - -
157A CYS* 3.8 0.2 - - - +
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Residues in contact with GLN 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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103A MET* 2.8 26.8 + - - +
104A HIS* 3.9 20.1 - - + +
106A TYR* 1.3 78.3 - - + +
108A SER* 1.3 56.9 + - - +
110A LEU* 3.4 10.0 + - + +
111A GLU* 3.0 41.1 + - - +
151A LEU* 3.2 50.5 + - - +
153A ARG* 4.1 16.6 - - + +
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Residues in contact with SER 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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74A PHE* 3.6 37.0 - - - -
78A ARG* 4.6 4.1 + - - -
104A HIS* 2.7 23.5 + - - +
105A TYR 3.7 0.2 - - - -
106A TYR 3.3 0.2 - - - -
107A GLN* 1.3 72.1 - - - +
109A CYS* 1.3 59.8 + - - +
111A GLU* 3.5 11.8 + - - +
112A ALA* 3.1 27.7 + - - +
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Residues in contact with CYS 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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13A MET* 3.5 33.7 - - - -
70A MET* 4.9 2.7 - - - -
74A PHE* 3.6 16.4 - - - -
82A PHE* 4.0 12.4 - - + -
88A LEU* 4.3 13.5 - - + -
90A TYR* 3.9 20.0 - - + -
105A TYR 3.1 15.8 + - - -
106A TYR* 3.1 9.7 + - + +
108A SER* 1.3 72.6 - - - +
110A LEU* 1.3 58.3 + - - +
112A ALA* 3.2 3.5 + - - +
113A ILE* 2.8 34.9 + - - +
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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
----------------------------------------------------------
88A LEU* 4.8 4.9 - - + -
106A TYR* 3.0 56.5 + - + +
107A GLN* 3.4 12.5 + - + +
109A CYS* 1.3 74.2 - - - +
111A GLU* 1.3 54.2 + - + +
113A ILE* 3.3 5.9 + - + +
114A LEU* 2.8 35.6 + - - +
122A ILE* 3.8 29.6 - - + -
151A LEU 4.0 5.4 - - - +
152A SER* 3.6 30.1 - - - +
153A ARG* 5.4 2.2 - - + -
155A LEU* 3.9 18.6 - - + +
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Residues in contact with GLU 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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78A ARG* 3.9 8.5 - - - +
107A GLN* 3.0 28.6 + - - +
108A SER* 4.0 9.8 + - - +
109A CYS 3.2 0.4 - - - -
110A LEU* 1.3 76.5 - - + +
112A ALA* 1.3 63.1 + - - +
114A LEU* 3.5 10.6 + - + +
115A GLN* 3.3 33.5 + - - +
153A ARG* 6.1 1.2 - - - +
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Residues in contact with ALA 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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74A PHE* 5.1 0.4 - - + -
78A ARG* 3.3 32.9 - - + +
82A PHE* 3.5 37.9 - - + +
108A SER 3.1 15.8 + - - +
109A CYS 3.8 1.8 - - - +
111A GLU* 1.3 76.8 - - - +
113A ILE* 1.3 57.2 + - - +
115A GLN* 4.2 2.2 - - - -
116A ASN* 3.2 34.0 + - - +
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Residues in contact with ILE 113 (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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11A LEU* 4.5 2.2 - - + -
82A PHE* 4.0 19.3 - - + +
85A VAL* 3.9 36.1 - - + -
88A LEU* 3.9 22.0 - - + -
109A CYS 2.8 18.4 + - - +
110A LEU* 3.7 7.0 - - - +
112A ALA* 1.3 75.0 - - - +
114A LEU* 1.3 60.0 + - - +
115A GLN 3.2 0.2 - - - -
116A ASN 4.5 0.2 - - - +
117A SER* 2.8 56.1 + - - +
118A PRO* 5.0 1.6 - - + +
120A ALA* 4.1 11.0 - - + -
122A ILE* 4.2 16.6 - - + -
155A LEU* 4.3 9.9 - - + -
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Residues in contact with LEU 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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110A LEU 2.8 17.5 + - - +
111A GLU* 3.8 11.0 - - + +
112A ALA 3.5 0.2 - - - -
113A ILE* 1.3 78.9 - - - +
115A GLN* 1.3 59.9 + - + +
118A PRO* 3.6 32.6 - - + +
154A PRO* 4.0 27.8 - - + -
155A LEU* 4.0 26.5 - - + -
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Residues in contact with GLN 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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78A ARG* 3.0 34.2 + - - +
111A GLU* 3.3 21.6 + - - +
112A ALA 3.9 0.4 - - - +
113A ILE 3.2 0.4 - - - -
114A LEU* 1.3 78.8 - - + +
116A ASN* 1.3 71.4 + - - +
118A PRO* 4.9 2.6 - - - +
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Residues in contact with ASN 116 (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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78A ARG* 4.4 14.2 - - - +
79A ASP* 3.8 13.0 - - - +
82A PHE* 3.4 25.9 - - - +
83A ARG* 3.5 32.9 + - - +
84A ASN 4.2 1.9 + - - -
112A ALA* 3.2 16.1 + - - +
115A GLN* 1.3 102.9 + - - +
117A SER* 1.3 68.0 + - - +
118A PRO* 3.8 3.9 - - - +
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Residues in contact with SER 117 (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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82A PHE 2.9 14.3 + - - -
84A ASN* 3.2 3.3 + - - -
85A VAL* 2.9 47.5 + - - -
113A ILE* 2.8 18.5 + - - +
116A ASN* 1.3 84.5 + - - +
118A PRO* 1.3 70.8 - - - +
119A ASP 3.2 2.9 - - - -
120A ALA* 3.1 17.4 + - - +
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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