Contacts of the helix formed by residues 99 - 113 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B GLY 3.5 3.8 + - - -
98B THR* 1.3 72.5 - - - +
100B ALA* 1.3 58.7 + - - +
101B ASP* 2.6 42.1 + - - +
102B ILE* 2.8 26.6 + - + +
103B ALA* 2.9 28.8 + - - +
102C ILE* 3.9 17.5 - - - +
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Residues in contact with ALA 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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41B PRO* 4.4 18.6 - - + -
43B VAL* 4.9 2.4 - - + +
98B THR 3.1 7.6 + - - +
99B ASP* 1.3 72.7 + - - +
101B ASP* 1.3 57.7 + - - +
103B ALA* 3.8 7.1 - - - +
104B GLN* 3.1 28.1 + - - +
131B LYS* 3.6 32.6 - - + +
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Residues in contact with ASP 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 ASP* 2.6 23.8 + - - +
100B ALA* 1.3 70.9 - - - +
102B ILE* 1.3 57.6 + - - +
104B GLN 3.3 0.7 + - - -
105B VAL 3.0 22.9 + - - -
131B LYS* 2.6 32.1 + - - +
73C ASP* 5.5 0.2 - - - +
102C ILE* 4.0 17.5 - - + +
105C VAL* 3.7 19.2 - - + +
106C GLN* 3.2 33.2 + - - +
109C ASN* 3.2 11.6 + - - +
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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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99A ASP* 5.5 1.3 - - - +
101A ASP* 4.3 22.2 - - + +
102A ILE* 4.2 25.4 - - + -
105A VAL* 5.3 2.5 - - + -
73B ASP* 6.2 0.2 - - + -
98B THR* 6.1 1.8 - - + -
99B ASP* 2.8 33.9 + - + +
101B ASP* 1.3 70.5 - - - +
103B ALA* 1.3 68.5 + - - +
105B VAL* 3.2 13.2 + - + +
106B GLN* 3.0 49.5 + - + +
102C ILE* 4.6 11.9 - - + -
105C VAL* 4.8 5.8 - - + -
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Residues in contact with ALA 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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41B PRO* 5.8 1.8 - - + -
43B VAL* 4.2 5.4 - - + -
73B ASP 5.5 0.9 - - - -
94B PHE* 3.9 40.7 - - + -
98B THR* 4.1 8.9 - - + +
99B ASP 2.9 17.7 + - - +
100B ALA* 3.9 7.2 - - - +
102B ILE* 1.3 79.7 - - - +
104B GLN* 1.3 62.3 + - - +
106B GLN* 3.3 7.6 + - - +
107B VAL* 3.1 27.2 + - - +
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Residues in contact with GLN 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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43B VAL* 4.0 17.4 - - + +
100B ALA 3.1 17.6 + - - +
103B ALA* 1.3 77.6 - - - +
105B VAL* 1.3 59.0 + - - +
107B VAL* 3.5 1.0 + - - +
108B GLN* 2.9 28.6 + - - +
129B VAL* 2.9 37.7 + - + +
130B GLU* 4.1 1.4 - - - +
131B LYS* 2.9 45.2 + - + +
109C ASN* 3.4 40.7 + - - +
112C GLN* 5.1 0.4 + - - +
113C LEU* 5.7 0.4 - - - +
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Residues in contact with VAL 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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105A VAL* 4.0 41.5 - - + -
101B ASP 3.0 14.5 + - - +
102B ILE* 3.5 17.9 - - + +
104B GLN* 1.3 78.4 - - - +
106B GLN* 1.3 67.4 + - + +
108B GLN* 4.0 15.0 - - - +
109B ASN* 2.9 32.7 + - - +
105C VAL* 4.0 16.8 - - + -
108C GLN* 4.2 8.3 - - + +
109C ASN* 3.4 18.1 + - - +
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Residues in contact with GLN 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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101A ASP* 3.2 29.6 + - - +
104A GLN* 4.0 15.0 + - - +
131A LYS* 4.0 14.8 - - - +
71B GLY 5.3 1.2 + - - -
72B ILE* 3.9 18.1 - - + +
73B ASP* 2.9 44.2 + - - +
102B ILE* 3.0 29.8 + - + +
103B ALA* 3.9 6.0 - - - +
105B VAL* 1.3 79.9 - - + +
107B VAL* 1.3 62.0 + - - +
109B ASN* 3.5 5.9 + - - +
110B LYS* 3.1 30.3 + - - +
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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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43B VAL* 4.3 11.7 - - + -
45B ILE* 3.4 35.9 - - + -
69B MET* 3.9 8.0 - - - +
72B ILE* 3.9 18.4 - - + -
92B LEU* 4.1 8.7 - - + -
94B PHE* 3.6 26.2 - - + -
103B ALA 3.1 17.1 + - - +
104B GLN 3.9 3.1 - - - +
106B GLN* 1.3 79.0 - - - +
108B GLN* 1.3 61.8 + - - +
110B LYS 3.4 0.7 + - - -
111B LEU* 3.1 21.5 + - - +
129B VAL* 4.1 9.9 - - + -
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Residues in contact with GLN 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 GLN* 2.9 17.6 + - + +
105B VAL* 3.9 5.8 - - - +
107B VAL* 1.3 77.7 - - - +
109B ASN* 1.3 74.2 + - - +
111B LEU* 3.5 8.2 - - - +
112B GLN* 3.1 34.8 + - + +
129B VAL* 4.2 17.0 - - + +
108C GLN* 3.3 25.1 + - - +
109C ASN* 2.7 46.1 + - - +
112C GLN* 3.8 28.9 - - + +
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Residues in contact with ASN 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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104A GLN* 4.8 6.7 + - - +
105A VAL* 4.1 33.9 - - - +
108A GLN* 3.0 48.8 + - - +
105B VAL* 2.9 23.4 + - - +
106B GLN* 3.9 6.3 - - - +
108B GLN* 1.3 95.8 - - - +
110B LYS* 1.3 65.2 + - + +
112B GLN* 3.2 25.0 + - - +
113B LEU* 3.6 2.8 - - - +
108C GLN* 3.6 6.7 + - - +
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Residues in contact with LYS 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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104A GLN* 3.8 14.3 - - - +
108A GLN* 4.6 5.7 + - - -
128A SER* 5.3 2.2 - - - +
129A VAL 2.8 36.4 + - - +
130A GLU* 5.0 4.2 - - - +
68B ASN* 3.3 26.2 - - - +
69B MET* 3.6 12.6 - - + -
70B ASN* 3.7 26.7 - - + +
71B GLY* 4.9 7.4 - - - -
72B ILE* 4.1 7.4 - - + -
106B GLN* 3.1 18.9 + - - +
107B VAL 3.4 0.2 + - - -
108B GLN 3.4 0.2 - - - -
109B ASN* 1.3 75.3 - - - +
111B LEU* 1.3 67.5 + - - +
113B LEU* 3.5 20.4 + - + +
114B ALA* 3.4 15.6 + - - +
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Residues in contact with LEU 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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45B ILE* 4.1 14.8 - - + -
65B ILE* 4.1 29.6 - - + -
69B MET* 3.9 5.5 - - + +
107B VAL 3.1 17.3 + - - +
108B GLN* 3.5 7.0 - - - +
110B LYS* 1.3 74.5 - - - +
112B GLN* 1.3 56.5 + - - +
114B ALA* 2.6 33.1 + - + +
115B MET* 3.0 29.3 + - + +
118B LEU* 4.7 0.4 - - + -
127B VAL* 3.8 27.6 - - + +
129B VAL* 3.7 25.1 - - + -
112C GLN* 5.1 2.2 - - + +
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Residues in contact with GLN 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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108A GLN* 4.1 14.7 + - - +
109A ASN* 6.2 0.2 - - - +
112A GLN* 3.2 38.8 - - + +
115A MET* 5.5 2.4 - - - +
108B GLN* 3.1 27.4 + - + +
109B ASN* 3.2 34.7 + - - +
110B LYS 3.3 0.4 - - - -
111B LEU* 1.3 75.4 - - - +
113B LEU* 1.3 62.0 + - + +
115B MET* 3.3 26.1 + - + +
116B PRO* 3.8 4.3 - - - +
108C GLN* 4.6 5.3 - - - +
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Residues in contact with LEU 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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108A GLN* 3.2 35.2 - - + +
111A LEU* 4.1 20.2 - - + -
112A GLN* 6.3 0.4 - - + -
115A MET* 4.9 16.9 - - + +
126A GLY* 4.4 12.4 - - - -
127A VAL* 3.1 35.6 + - + +
128A SER* 4.2 1.6 - - - -
129A VAL* 4.2 14.6 - - + +
68B ASN* 4.5 6.2 - - - +
109B ASN 3.6 4.7 - - - +
110B LYS* 3.5 21.5 + - + +
111B LEU 3.1 0.8 - - - -
112B GLN* 1.3 83.1 - - + +
114B ALA* 1.3 58.3 + - - +
115B MET 3.4 0.2 - - - -
116B PRO* 3.5 13.6 - - - +
117B LEU* 4.2 8.1 - - - +
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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