Contacts of the helix formed by residues 99 - 115 (chain C) in PDB entry 5NC5
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 ASP 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C GLY 3.5 3.0 + - - -
98C THR* 1.3 74.7 - - + +
100C ALA* 1.3 63.7 + - - +
101C ASP* 2.9 24.2 + - - +
102C ILE* 3.1 31.7 + - + +
103C ALA* 2.9 21.3 + - - +
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Residues in contact with ALA 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PRO* 4.0 22.9 - - + -
42C ALA 6.0 0.7 - - - +
43C VAL* 4.7 2.0 - - + +
98C THR 3.1 5.9 + - - +
99C ASP* 1.3 73.0 + - - +
101C ASP* 1.4 52.3 + - - +
103C ALA* 3.1 8.5 + - - +
104C GLN* 2.8 35.3 + - - +
131C LYS* 3.5 28.6 - - + +
295C THR* 4.2 14.6 - - + -
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Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASP* 4.1 1.2 - - - +
102A ILE* 4.2 29.7 - - + +
106A GLN* 3.7 14.6 + - - -
99C ASP* 2.9 13.5 + - - +
100C ALA* 1.4 77.8 - - - +
102C ILE* 1.3 58.1 + - + +
104C GLN* 3.5 8.2 - - - +
105C VAL* 3.1 28.8 + - - +
131C LYS* 2.8 31.2 + - - -
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Residues in contact with ILE 102 (chain C).
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* 5.9 2.5 - - + -
99B ASP* 3.9 22.0 - - - +
101B ASP* 4.0 21.1 - - + +
102B ILE* 4.6 15.7 - - + -
98C THR* 6.2 0.4 - - + -
99C ASP* 3.1 30.7 + - + +
101C ASP* 1.3 75.2 - - + +
103C ALA* 1.3 62.8 + - - +
105C VAL* 3.0 6.7 + - + +
106C GLN* 2.8 45.9 + - + +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PRO* 5.8 0.9 - - + -
43C VAL* 4.3 6.1 - - + -
73C ASP 5.7 0.4 - - - -
94C PHE* 3.8 44.1 - - + -
98C THR* 4.1 7.5 - - + +
99C ASP 2.9 13.9 + - - +
100C ALA* 3.4 11.0 - - - +
102C ILE* 1.3 74.3 - - - +
104C GLN* 1.3 64.8 + - - +
106C GLN* 3.2 8.3 + - - +
107C VAL* 3.0 27.2 + - - +
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Residues in contact with GLN 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 4.3 5.6 - - - +
106A GLN* 6.2 5.2 - - + -
109A ASN* 4.9 2.2 + - - +
43C VAL* 3.9 15.6 - - + +
100C ALA 2.8 13.3 + - - +
101C ASP* 3.5 11.1 - - - +
103C ALA* 1.3 77.8 - - - +
105C VAL* 1.3 79.0 + - - +
107C VAL* 3.3 1.7 + - - +
108C GLN* 2.5 49.0 + - - +
129C VAL* 3.4 33.5 + - + +
130C GLU* 4.8 0.2 - - - -
131C LYS* 4.4 22.0 - - + +
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Residues in contact with VAL 105 (chain C).
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* 4.2 18.4 - - + -
105A VAL* 4.3 14.8 - - + -
101B ASP* 3.7 38.1 - - + +
102B ILE* 4.6 6.7 - - + +
105B VAL* 4.0 18.2 - - + -
101C ASP 3.1 11.3 + - - +
102C ILE* 3.0 12.1 + - + +
104C GLN* 1.3 91.6 + - - +
106C GLN* 1.3 64.6 + - - +
108C GLN* 3.2 6.1 + - - +
109C ASN* 2.9 24.8 + - - +
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASP* 3.2 34.3 + - + +
131B LYS* 5.0 1.9 - - - +
72C ILE* 3.6 16.5 - - + +
73C ASP* 3.1 57.7 + - - +
102C ILE* 2.8 33.8 + - + +
103C ALA* 3.2 6.2 + - - +
105C VAL* 1.3 77.3 - - - +
107C VAL* 1.3 62.4 + - - +
109C ASN* 3.3 8.5 + - - +
110C LYS* 3.1 26.0 + - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 4.1 15.0 - - + -
45C ILE* 3.7 27.4 - - + -
69C MET* 4.2 5.8 - - - -
72C ILE* 4.4 9.2 - - + -
92C LEU* 4.2 16.6 - - + -
94C PHE* 4.0 21.5 - - + -
103C ALA 3.0 16.9 + - - +
104C GLN 3.7 3.4 - - - +
106C GLN* 1.3 77.5 - - - +
108C GLN* 1.3 64.8 + - - +
110C LYS* 3.1 2.9 + - - +
111C LEU* 2.8 22.2 + - - +
129C VAL* 3.7 20.2 - - + -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 3.7 28.5 + - - +
108A GLN 5.6 0.2 - - - -
109A ASN* 4.1 22.2 + - - +
112A GLN* 6.2 0.2 - - - +
105B VAL* 4.2 3.3 - - + +
108B GLN* 3.3 29.7 + - - +
109B ASN* 3.6 13.7 + - - +
112B GLN* 4.6 5.8 - - - +
104C GLN* 2.5 50.9 + - - +
105C VAL* 3.5 7.0 - - - +
107C VAL* 1.3 77.9 - - - +
109C ASN* 1.3 60.1 + - - +
111C LEU* 3.4 7.7 + - - +
112C GLN* 3.1 18.2 + - - +
129C VAL* 4.1 10.2 - - + +
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Residues in contact with ASN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASP* 3.2 30.9 + - - +
104B GLN* 3.4 42.7 + - - +
105B VAL* 3.4 16.3 + - - +
108B GLN* 2.7 30.1 + - - +
131B LYS* 4.2 5.3 - - - +
105C VAL* 2.9 22.1 + - - +
106C GLN* 3.7 6.8 - - - +
107C VAL 3.1 0.2 - - - -
108C GLN* 1.3 75.3 - - - +
110C LYS* 1.3 66.3 + - + +
112C GLN* 3.6 14.0 - - - +
113C LEU* 4.0 8.5 + - - +
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B GLY 3.8 13.9 + - - -
174B ASP* 4.3 10.0 + - - -
68C ASN* 3.4 32.0 - - - +
69C MET* 3.9 12.1 - - + -
70C ASN* 2.4 40.4 + - - +
71C GLY 4.1 6.4 + - - -
72C ILE* 3.9 17.9 - - + -
106C GLN 3.1 18.6 + - - +
107C VAL 3.9 2.2 - - - +
109C ASN* 1.3 75.7 - - + +
111C LEU* 1.3 65.6 + - - +
113C LEU* 3.2 36.4 + - + +
114C ALA 3.8 2.4 + - - -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 3.5 22.0 - - + -
65C ILE* 3.9 31.4 - - + -
69C MET* 3.5 9.5 - - + +
107C VAL 2.8 20.4 + - - +
108C GLN* 3.6 8.5 - - + +
110C LYS* 1.3 68.7 - - - +
112C GLN* 1.3 57.9 + - - +
113C LEU 3.0 2.9 - - - -
114C ALA* 2.7 28.8 + - + -
115C MET* 3.0 29.1 + - + +
118C LEU* 5.4 1.1 - - + -
127C VAL* 4.1 14.1 - - + +
129C VAL* 3.3 30.3 - - + -
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Residues in contact with GLN 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 5.8 0.2 - - - +
108B GLN* 3.8 33.0 - - + +
111B LEU* 5.1 2.1 - - + +
127B VAL 2.5 31.3 + - - -
128B SER* 3.6 3.4 - - - +
129B VAL* 3.1 35.8 + - + +
108C GLN 3.1 13.1 + - - +
109C ASN 3.6 10.9 - - - +
110C LYS 3.3 0.2 - - - -
111C LEU* 1.3 76.6 - - - +
113C LEU* 1.3 80.0 + - - +
114C ALA 3.4 0.2 + - - -
115C MET* 3.6 11.3 + - - +
116C PRO* 3.4 17.3 - - - +
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B SER* 4.3 10.3 - - - +
129B VAL 4.0 6.7 - - - +
130B GLU* 3.8 31.0 - - + +
174B ASP* 6.0 1.6 - - - +
68C ASN* 3.7 20.8 - - - +
109C ASN 4.0 6.3 - - - +
110C LYS* 3.2 34.1 + - + +
111C LEU 3.0 1.2 - - - -
112C GLN* 1.3 97.1 - - - +
114C ALA* 1.3 59.7 + - - +
116C PRO* 3.8 10.0 - - - +
117C LEU* 3.5 15.4 - - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C VAL* 3.9 15.5 - - + +
65C ILE* 4.2 11.0 - - + -
68C ASN* 3.8 22.2 - - + +
110C LYS 3.8 1.0 + - - +
111C LEU* 2.7 23.3 + - + +
113C LEU* 1.3 81.2 - - - +
115C MET* 1.3 55.5 + - - +
116C PRO* 3.3 1.3 - - - -
117C LEU* 2.8 34.0 + - - +
118C LEU* 3.6 8.8 + - + +
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Residues in contact with MET 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 5.5 5.8 - - - +
111C LEU* 3.0 26.9 + - + +
112C GLN* 3.6 11.4 + - - +
114C ALA* 1.3 75.8 - - - +
116C PRO* 1.3 66.5 - - + +
117C LEU 3.1 0.7 + - - -
118C LEU* 3.4 23.0 + - + +
123C GLN* 2.9 67.6 + - + +
126C GLY* 5.9 0.2 - - - -
127C VAL* 4.0 24.7 - - + +
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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
------------------------------------------------------------
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