Contacts of the helix formed by residues 99 - 115 (chain B) in PDB entry 6DMY
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 THR 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 4.2 21.8 - - + +
76B LEU* 3.7 9.9 - - + -
98B MET* 1.3 76.0 - - - +
100B GLN* 1.3 57.3 + - - +
101B ARG* 4.3 1.7 + - - +
102B CYS* 3.1 11.3 + - - +
103B LYS* 2.8 32.4 + - - +
142B GLU 3.5 24.7 - - - +
143B GLY 2.8 17.8 + - - +
144B ARG* 3.5 19.1 - - + +
185B VAL* 4.5 1.6 - - - +
188B GLU* 4.2 14.0 + - - +
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU* 4.8 25.4 + - + +
99B THR* 1.3 76.9 - - - +
101B ARG* 1.3 58.8 + - - +
103B LYS* 3.4 27.5 + - - +
104B ASP* 3.0 28.9 + - - +
188B GLU* 3.9 19.2 + - - +
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Residues in contact with ARG 101 (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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99B THR* 3.3 3.2 + - - +
100B GLN* 1.3 77.8 - - - +
102B CYS* 1.3 57.4 + - - +
104B ASP* 3.3 5.0 + - - +
105B LYS* 2.9 51.8 + - + +
169B GLY 5.1 2.6 + - - -
171B ASP* 3.1 33.9 + - - -
185B VAL* 3.9 16.8 - - + +
186B LYS* 3.4 43.3 - - - +
188B GLU* 4.7 20.7 + - - +
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Residues in contact with CYS 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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98B MET* 3.9 15.9 - - + -
99B THR* 3.1 13.6 + - - +
101B ARG* 1.3 77.6 - - - +
103B LYS* 1.3 58.9 + - - +
105B LYS* 4.6 0.4 - - - +
106B LEU* 2.9 35.9 + - - +
143B GLY 3.8 15.9 - - - +
144B ARG* 4.4 9.4 - - - -
146B VAL* 3.9 37.9 - - - -
170B PHE* 4.7 6.5 - - - -
185B VAL* 3.9 19.0 - - + +
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Residues in contact with LYS 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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75B GLU 5.1 0.8 + - - -
77B THR* 3.4 36.7 - - + +
78B PRO 5.1 0.7 - - - +
79B ASN* 4.3 17.7 + - - +
98B MET* 3.7 27.6 - - + +
99B THR 2.8 17.4 + - - +
100B GLN* 3.6 36.1 - - - +
101B ARG 3.3 0.2 - - - -
102B CYS* 1.3 73.8 - - - +
104B ASP* 1.3 54.1 + - - +
106B LEU* 3.9 0.5 - - - +
107B ASN* 2.7 46.3 + - - +
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Residues in contact with ASP 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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100B GLN 3.0 17.4 + - - +
101B ARG* 3.3 5.8 + - - +
103B LYS* 1.3 77.0 - - - +
105B LYS* 1.3 88.3 + - - +
107B ASN* 3.2 9.8 + - - +
108B ALA* 3.0 22.7 + - - +
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Residues in contact with LYS 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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101B ARG* 2.9 38.1 + - + +
104B ASP* 1.3 105.2 + - - +
106B LEU* 1.3 58.2 + - - +
108B ALA* 3.4 8.9 + - - +
109B LEU* 2.9 28.1 + - - +
168B ALA* 4.6 6.0 + - - +
169B GLY* 3.3 42.9 - - - +
170B PHE* 3.8 21.3 - - + -
185B VAL* 4.2 10.5 - - + -
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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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79B ASN* 3.9 11.0 - - - +
84B ILE* 4.1 12.1 - - + -
86B PHE* 4.9 1.3 - - + -
98B MET* 3.7 30.3 - - + -
102B CYS* 2.9 21.4 + - - +
103B LYS* 4.0 3.1 - - - +
105B LYS* 1.3 76.2 - - - +
107B ASN* 1.3 59.1 + - - +
109B LEU* 3.2 1.0 + - + +
110B ALA* 2.9 28.4 + - - +
122B LEU* 3.9 20.9 - - + -
124B VAL* 3.8 28.5 - - + -
146B VAL* 4.3 10.1 - - + -
148B ILE* 4.5 4.5 - - + -
170B PHE* 3.9 21.2 - - + -
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 3.8 24.3 + - - +
81B ASN* 3.0 31.4 + - - +
84B ILE* 4.5 0.2 - - - +
103B LYS* 2.7 31.7 + - - +
104B ASP* 3.5 8.2 + - - +
106B LEU* 1.3 75.9 - - - +
108B ALA* 1.3 62.2 + - - +
110B ALA* 3.3 3.6 + - - +
111B ILE* 3.0 34.3 + - + +
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Residues in contact with ALA 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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104B ASP* 3.0 13.8 + - - +
105B LYS* 3.7 12.1 - - - +
106B LEU 3.3 0.2 - - - -
107B ASN* 1.3 74.8 - - - +
109B LEU* 1.3 59.1 + - - +
111B ILE* 3.4 12.8 + - - +
112B SER* 3.0 28.1 + - - -
168B ALA* 4.1 20.1 - - + +
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Residues in contact with LEU 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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105B LYS 2.9 18.3 + - - +
106B LEU* 3.6 7.0 - - + +
107B ASN 3.2 0.4 - - - -
108B ALA* 1.3 75.4 - - - +
110B ALA* 1.3 59.4 + - - +
112B SER* 3.2 3.3 + - - +
113B VAL* 2.9 40.9 + - + +
122B LEU* 3.7 17.0 - - + -
148B ILE* 3.7 29.6 - - + -
161B LEU 4.6 1.1 - - - +
164B LEU* 3.4 43.1 - - + +
165B ALA* 3.8 5.4 - - + +
168B ALA* 3.7 9.4 - - + +
170B PHE* 3.6 25.6 - - + -
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Residues in contact with ALA 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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81B ASN* 4.6 8.3 - - - +
83B ASP* 5.2 3.6 - - + -
84B ILE* 4.0 26.7 - - + -
106B LEU 2.9 16.7 + - - +
107B ASN 3.7 4.9 - - - +
109B LEU* 1.3 75.4 - - - +
111B ILE* 1.3 63.6 + - + +
113B VAL* 3.3 1.0 + - - +
114B MET* 3.1 38.8 + - + +
122B LEU* 3.7 20.2 - - + +
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Residues in contact with ILE 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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81B ASN* 5.8 4.0 - - - +
107B ASN* 3.0 22.2 + - + +
108B ALA* 3.5 11.7 - - - +
109B LEU 3.3 0.2 - - - -
110B ALA* 1.3 77.1 - - + +
112B SER* 1.3 56.8 + - - +
114B MET* 3.6 11.3 + - + +
115B ASN* 2.8 46.6 + - - +
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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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108B ALA 3.0 15.6 + - - -
109B LEU* 3.2 10.9 + - - -
111B ILE* 1.3 76.4 - - - +
113B VAL* 1.3 61.5 + - - +
115B ASN* 3.0 14.2 + - - +
116B GLN* 3.0 25.8 + - - +
164B LEU* 3.3 26.4 - - - +
167B GLU 5.5 2.3 + - - -
168B ALA* 5.2 5.4 - - - -
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Residues in contact with VAL 113 (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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109B LEU* 2.9 30.9 + - + +
110B ALA 3.9 3.1 - - - +
112B SER* 1.3 77.1 - - - +
114B MET* 1.3 59.0 + - - +
116B GLN* 2.8 20.9 + - - +
117B TRP* 3.2 29.8 + - + +
120B VAL* 4.1 19.3 - - + +
122B LEU* 4.0 29.4 - - + +
150B THR* 5.3 2.0 - - + -
161B LEU* 3.7 26.9 - - + -
164B LEU* 4.3 9.4 - - + -
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Residues in contact with MET 114 (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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83B ASP* 3.3 46.7 - - + +
110B ALA* 3.1 26.0 + - + +
111B ILE* 4.1 10.5 - - + +
113B VAL* 1.3 76.4 - - + +
115B ASN* 1.3 60.9 + - - +
116B GLN 3.1 0.8 - - - -
117B TRP 3.4 20.1 + - - +
118B PRO* 5.2 0.7 - - - +
120B VAL 3.7 18.8 - - - +
121B LYS* 4.8 13.9 - - + -
122B LEU 5.5 1.1 - - - +
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Residues in contact with ASN 115 (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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111B ILE* 2.8 42.0 + - - +
112B SER* 3.0 15.8 + - - +
114B MET* 1.3 75.4 - - - +
116B GLN* 1.3 60.2 + - - +
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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