Contacts of the helix formed by residues 96 - 113 (chain C) in PDB entry 2NP5
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 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C PRO 3.5 0.4 - - - -
95C LEU* 1.3 77.5 - - - +
97C GLU* 1.3 58.6 + - - +
98C ALA* 3.5 8.4 + - - +
99C ARG* 2.9 59.9 + - - +
100C SER* 2.8 30.0 + - - -
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Residues in contact with GLU 97 (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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96C ASP* 1.3 73.9 - - - +
98C ALA* 1.3 63.3 + - - +
100C SER* 3.3 13.8 + - - -
101C ARG* 3.0 62.4 + - - +
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Residues in contact with ALA 98 (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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19C PHE* 4.9 0.3 - - - -
96C ASP* 3.3 10.4 + - - +
97C GLU* 1.3 77.9 - - - +
99C ARG* 1.3 60.8 + - + +
101C ARG* 3.4 24.7 + - - +
102C GLU* 3.1 39.3 + - - +
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Residues in contact with ARG 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG* 4.0 4.7 - - - +
90C SER* 2.9 40.7 + - - -
91C GLN* 3.7 35.9 + - - +
92C LEU 5.3 0.5 - - - +
93C LEU 3.3 14.4 - - - +
94C PRO* 3.9 3.0 - - - +
95C LEU* 3.7 28.2 - - - +
96C ASP* 2.9 40.4 + - - +
98C ALA* 1.3 76.7 - - + +
100C SER* 1.3 60.8 + - - +
102C GLU* 3.8 16.2 - - - +
103C ALA* 2.9 31.4 + - - +
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Residues in contact with SER 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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94C PRO* 3.6 24.4 - - - +
96C ASP 2.8 18.4 + - - -
97C GLU* 3.6 17.9 + - - -
99C ARG* 1.3 75.5 - - - +
101C ARG* 1.3 59.2 + - - +
103C ALA* 3.4 2.3 + - - +
104C HIS* 2.9 30.4 + - - +
165C ILE* 4.3 6.1 - - - +
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Residues in contact with ARG 101 (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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19C PHE* 3.8 16.1 - - + -
20C ASP* 6.0 1.3 - - - -
23C ALA* 3.9 28.7 - - + +
97C GLU* 3.0 54.1 + - - +
98C ALA* 3.6 27.9 + - - +
100C SER* 1.3 76.6 - - - +
102C GLU* 1.3 61.6 + - - +
104C HIS* 3.4 5.8 + - - +
105C VAL* 3.0 29.3 + - - +
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Residues in contact with GLU 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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19C PHE* 3.7 24.2 - - + -
64C LEU* 4.6 15.2 - - + +
71C ARG* 2.6 48.4 + - - -
91C GLN 4.2 1.9 - - - +
98C ALA* 3.1 26.3 + - - +
99C ARG* 3.8 12.9 - - - +
100C SER 3.4 0.2 - - - -
101C ARG* 1.3 77.9 - - - +
103C ALA* 1.3 57.4 + - - +
105C VAL* 3.2 1.7 + - - +
106C MSE 2.8 33.6 + - - +
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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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92C LEU 4.1 19.7 - - - +
94C PRO* 4.3 9.0 - - + -
99C ARG 2.9 19.6 + - - +
100C SER 3.8 3.4 - - - +
102C GLU* 1.3 75.8 - - - +
104C HIS* 1.3 59.4 + - - +
106C MSE 4.0 5.4 - - - +
107C ALA* 3.0 32.2 + - - +
161C ALA* 4.4 11.5 - - + +
165C ILE* 4.0 15.6 - - + +
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Residues in contact with HIS 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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111A VAL* 4.0 19.7 + - + +
114A ALA* 3.7 24.9 - - + +
115A THR* 3.7 24.9 - - + +
22C ALA 3.4 17.1 + - - -
23C ALA* 3.1 30.1 + - - +
26C GLY* 4.1 10.8 - - - -
100C SER 2.9 18.5 + - - +
101C ARG* 3.5 7.4 - - - +
103C ALA* 1.3 77.3 - - - +
105C VAL* 1.3 57.3 + - - +
107C ALA* 3.9 1.9 - - - +
108C ALA* 3.1 24.5 + - + +
165C ILE* 4.0 16.3 - - + +
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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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19C PHE* 3.7 28.7 - - + +
22C ALA* 3.9 17.5 - - + -
23C ALA* 3.6 31.6 - - - +
27C LEU* 5.4 0.9 - - + -
64C LEU* 3.7 11.9 - - + -
101C ARG 3.0 17.6 + - - +
102C GLU 3.9 0.7 - - - +
104C HIS* 1.3 74.2 - - - +
106C MSE 1.3 66.7 + - - +
108C ALA* 3.1 7.6 + - + +
109C PHE* 2.9 49.6 + - + -
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Residues in contact with MSE 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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61C LEU* 3.9 24.0 - - + -
64C LEU* 2.7 53.2 - - + -
65C VAL* 4.5 9.9 - - + -
68C LEU* 5.5 8.1 - - + -
92C LEU* 5.9 7.2 - - + -
102C GLU 2.8 16.5 + - - +
103C ALA* 4.0 5.8 - - - +
105C VAL* 1.3 77.7 - - - +
107C ALA* 1.3 57.8 + - - +
109C PHE* 3.3 5.2 + - - +
110C ALA* 3.0 26.7 + - - +
123C ARG* 4.1 19.6 + - - +
126C THR* 6.0 2.2 - - - -
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Residues in contact with ALA 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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111A VAL* 3.8 17.9 - - + -
162A LEU* 4.6 8.4 - - + +
103C ALA 3.0 19.8 + - - +
104C HIS 3.9 0.4 - - - +
106C MSE 1.3 76.7 - - - +
108C ALA* 1.3 63.5 + - - +
110C ALA* 3.1 9.0 + - - +
111C VAL* 3.1 26.3 + - - +
161C ALA* 6.1 0.7 - - + -
162C LEU* 3.9 14.4 - - + +
165C ILE* 3.9 16.2 - - + -
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Residues in contact with ALA 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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111A VAL* 3.9 21.3 - - + +
22C ALA* 6.0 1.1 - - + +
26C GLY* 5.6 0.4 - - - -
27C LEU* 3.7 32.3 - - + +
104C HIS* 3.1 18.2 + - + +
105C VAL* 3.1 11.6 + - - +
107C ALA* 1.3 77.5 - - - +
109C PHE* 1.3 57.2 + - - +
111C VAL* 3.3 5.1 + - - +
112C ARG* 2.9 28.1 + - - +
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Residues in contact with PHE 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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18C LEU* 3.9 24.5 - - + -
27C LEU* 3.8 20.2 - - + +
57C PHE* 3.6 40.4 - + + -
60C ALA* 4.8 1.8 - - + -
61C LEU* 3.8 41.5 - - + -
64C LEU* 4.6 5.4 - - + -
105C VAL* 2.9 45.2 + - + -
106C MSE 3.6 7.2 - - - +
108C ALA* 1.3 75.0 - - - +
110C ALA* 1.3 58.1 + - - +
112C ARG* 3.2 2.7 + - - +
113C ALA* 2.9 29.3 + - - +
119C LEU* 3.8 25.8 - - + +
123C ARG* 5.5 0.7 - - - -
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Residues in contact with ALA 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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162A LEU* 3.9 25.1 - - + +
165A ILE* 3.8 13.5 - - - +
166A GLY 4.7 0.7 + - - -
106C MSE 3.0 14.1 + - - +
107C ALA* 3.1 8.5 + - - +
109C PHE* 1.3 76.9 - - - +
111C VAL* 1.3 61.5 + - - +
113C ALA* 3.4 15.5 - - - +
123C ARG* 3.5 42.1 - - - +
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Residues in contact with VAL 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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26A GLY* 5.9 1.6 - - - -
28A GLU* 5.7 4.9 - - - +
104A HIS* 4.2 17.0 + - + +
107A ALA* 3.8 24.7 - - + +
108A ALA* 3.9 26.9 - - + +
111A VAL* 3.6 21.8 - - + -
162A LEU* 4.0 7.2 - - + -
165A ILE* 4.5 6.1 - - + -
107C ALA 3.1 13.4 + - - +
108C ALA* 3.8 6.5 - - - +
110C ALA* 1.3 73.5 - - - +
112C ARG* 1.3 67.7 + - - +
114C ALA* 3.0 22.3 + - - +
115C THR* 5.6 0.2 - - - +
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Residues in contact with ARG 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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28A GLU* 3.1 49.5 + - - +
112A ARG* 4.9 1.0 - - - +
27C LEU* 3.8 36.7 + - + +
28C GLU* 4.0 2.4 - - - +
53C LYS* 4.4 13.9 - - - +
57C PHE* 3.8 27.2 - - + -
108C ALA 2.9 17.2 + - - +
109C PHE* 3.2 7.4 + - - +
111C VAL* 1.3 77.9 - - - +
113C ALA* 1.3 61.2 + - - +
115C THR* 3.0 26.2 + - - -
116C SER* 3.2 11.4 + - - -
119C LEU* 3.4 25.1 - - + -
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Residues in contact with ALA 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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166A GLY* 3.9 12.4 - - - -
601A NDS 2.8 29.1 - - - -
109C PHE 2.9 12.1 + - - +
110C ALA* 3.4 18.4 - - - +
111C VAL 3.1 0.2 - - - -
112C ARG* 1.3 76.3 - - - +
114C ALA* 1.3 56.7 + - - +
115C THR 3.1 0.5 + - - -
116C SER 3.4 11.0 + - - +
119C LEU* 4.0 6.5 - - - +
120C ALA* 3.6 28.0 - - - +
123C ARG* 5.1 5.8 - - + -
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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