Contacts of the helix formed by residues 99 - 111 (chain B) in PDB entry 6CM9
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 ASN 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B LEU* 3.9 16.8 - - - +
97B ASP* 3.2 22.5 + - - +
98B PRO* 1.3 76.2 - - - +
100B PRO* 1.3 76.8 - - - +
101B LEU* 3.6 10.0 + - - +
102B ILE* 3.2 21.8 - - + +
103B ARG* 3.6 3.5 + - - -
146M ALA 3.7 21.4 + - - -
147M PRO* 4.4 1.8 + - - +
148M ARG* 3.5 23.9 - - - +
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Residues in contact with PRO 100 (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 PRO 3.4 8.9 - - - +
99B ASN* 1.3 90.5 - - - +
101B LEU* 1.3 59.9 + - - +
102B ILE 3.3 0.2 - - - -
103B ARG* 3.4 23.7 + - - +
104B ALA* 2.9 30.0 + - - +
134B ASP* 3.2 33.9 - - + +
136B TYR* 4.2 9.5 - - + -
137B VAL* 4.5 5.8 - - + +
148M ARG* 3.5 22.4 - - - +
149M PRO* 3.8 16.6 - - + -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.8 12.3 - - + -
67B LYS* 4.2 19.1 - - - +
99B ASN* 3.3 10.4 + - - +
100B PRO* 1.3 81.8 - - - +
102B ILE* 1.3 57.6 + - - +
104B ALA* 3.4 0.9 + - - -
105B LEU* 2.9 28.4 + - + +
108B ARG* 5.0 4.9 - - - +
136B TYR* 3.8 27.6 - - + +
116M GLU* 4.8 3.4 - - - +
134M TYR* 4.5 19.5 - - + -
146M ALA* 3.8 22.2 - - + -
147M PRO 3.5 18.4 - - - +
149M PRO* 3.6 20.4 - - + -
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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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60B THR 5.7 1.6 - - - +
62B ASN 5.4 0.9 - - - +
63B LEU* 4.1 22.7 - - + -
66B LYS* 3.7 38.4 - - + -
70B TYR* 5.3 0.3 - - - -
94B ASP* 4.2 18.7 - - + +
97B ASP* 3.3 33.7 - - + +
99B ASN* 3.2 25.4 - - + +
101B LEU* 1.3 76.7 - - - +
103B ARG* 1.3 59.6 + - - +
105B LEU* 3.7 6.1 - - + +
106B ALA* 2.9 28.1 + - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP 3.8 17.5 - - - +
95B CYS* 4.2 16.7 - - - +
96B GLU 4.6 1.7 + - - -
97B ASP* 3.1 32.2 + - - +
98B PRO* 3.7 13.8 + - - +
99B ASN 3.6 4.8 + - - +
100B PRO* 3.4 28.4 + - - +
101B LEU 3.3 0.6 - - - -
102B ILE* 1.3 80.9 - - - +
104B ALA* 1.3 57.3 + - - +
106B ALA* 3.3 4.1 + - - +
107B VAL* 2.9 31.4 + - - +
128B LYS* 5.5 3.1 - - - +
129B CYS* 5.3 5.6 - - - -
132B ASP* 2.6 42.9 + - - -
133B GLU* 6.0 1.6 - - - +
134B ASP* 4.3 9.9 - - - +
137B VAL* 3.9 14.3 - - + +
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Residues in contact with ALA 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 PRO 2.9 17.8 + - - +
101B LEU 4.0 0.2 - - - +
103B ARG* 1.3 73.7 - - - +
105B LEU* 1.3 61.6 + - - +
107B VAL* 4.3 2.9 - - - +
108B ARG* 2.9 29.8 + - - +
136B TYR* 3.6 26.7 - - + -
137B VAL* 3.7 16.7 - - - +
140B THR* 3.4 27.8 - - - +
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Residues in contact with LEU 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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63B LEU* 4.0 20.0 - - + -
66B LYS* 4.5 1.8 - - + -
67B LYS* 3.7 40.2 - - + +
70B TYR* 3.6 27.1 - - + -
101B LEU* 2.9 21.0 + - + +
102B ILE* 3.7 4.7 - - - +
104B ALA* 1.3 74.1 - - - +
106B ALA* 1.3 54.5 + - - +
108B ARG* 3.5 13.8 + - + +
109B THR* 2.5 44.7 + - - +
115M ASP* 3.4 30.5 - - - +
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Residues in contact with ALA 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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70B TYR* 4.2 20.6 - - - +
91B PHE* 4.0 8.1 - - + +
94B ASP* 4.4 11.9 - - + +
95B CYS* 3.7 19.7 - - - -
102B ILE 2.9 18.1 + - - +
103B ARG 3.6 5.4 - - - +
105B LEU* 1.3 78.5 - - - +
107B VAL* 1.3 56.5 + - - +
109B THR* 3.2 5.6 + - - -
110B MET* 2.9 35.3 + - - +
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Residues in contact with VAL 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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95B CYS* 4.2 8.1 - - - -
103B ARG 2.9 20.3 + - - +
104B ALA* 3.9 5.6 - - - +
105B LEU 3.3 0.2 - - - -
106B ALA* 1.3 77.5 - - - +
108B ARG* 1.3 61.7 + - - +
109B THR 3.3 0.7 + - - -
110B MET* 3.3 18.3 + - + +
111B GLY 3.5 0.5 + - - -
125B PRO 5.4 0.7 - - - +
126B LEU* 4.0 6.3 - - + -
129B CYS* 3.7 32.1 - - + -
137B VAL* 4.2 4.9 - - + -
140B THR* 3.9 7.4 - - + -
141B ALA* 3.7 32.8 - - + +
144B CYS* 3.3 29.2 - - + -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 5.9 1.4 - - - +
74B MET* 4.0 2.7 - - + +
101B LEU* 5.0 4.4 - - - +
104B ALA 2.9 18.3 + - - +
105B LEU* 3.6 27.2 - - + +
107B VAL* 1.3 76.5 - - - +
109B THR* 1.3 59.4 + - - +
111B GLY 4.4 0.9 - - - -
112B CYS* 3.3 11.8 + - - -
136B TYR* 2.8 35.0 + - - -
140B THR* 3.7 20.5 + - + +
144B CYS* 5.3 2.0 - - - -
147B LYS* 3.2 26.0 + - - +
19M ARG* 5.5 0.9 - - - +
115M ASP* 3.5 40.3 + - - +
116M GLU* 3.7 13.0 + - - -
119M ASP* 3.2 31.4 + - - +
124M GLN* 3.8 15.2 - - - +
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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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70B TYR* 3.6 45.4 - - + +
73B LEU* 5.2 0.4 - - + -
74B MET* 4.0 13.8 - - + +
91B PHE* 3.6 25.4 - - + -
105B LEU* 2.5 29.3 + - - +
106B ALA 3.6 4.5 - - - -
107B VAL 3.1 0.2 - - - -
108B ARG* 1.3 78.6 - - - +
110B MET* 1.3 64.8 + - - +
111B GLY 3.3 0.9 - - - -
112B CYS* 3.3 11.3 + - - +
113B ILE* 3.6 18.3 + - + +
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Residues in contact with MET 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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91B PHE* 3.8 28.0 - - + -
95B CYS* 3.8 25.4 - - - -
106B ALA 2.9 22.6 + - - +
107B VAL* 3.3 13.0 + - - +
109B THR* 1.3 77.4 - - - +
111B GLY* 1.3 61.1 + - - +
113B ILE* 3.8 14.5 + - - +
119B THR* 5.4 2.8 - - - +
122B LEU* 3.4 63.4 - - + +
125B PRO* 3.7 17.3 - - + -
126B LEU* 4.2 18.8 - - + +
144B CYS* 4.8 2.7 - - - -
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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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107B VAL 3.5 7.9 + - - -
108B ARG 4.4 0.8 - - - -
109B THR 3.3 0.6 - - - -
110B MET* 1.3 79.7 - - - +
112B CYS* 1.3 61.9 + - - +
113B ILE 3.4 6.1 + - - +
119B THR* 6.5 0.2 - - - -
144B CYS* 3.9 12.0 - - - -
147B LYS* 3.8 33.1 - - - +
148B LEU* 5.4 4.0 - - - -
151B ILE* 4.0 15.6 - - - +
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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