Contacts of the strand formed by residues 153 - 162 (chain C) in PDB entry 2NVX
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 LEU 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C THR 3.1 14.6 - - - +
54C ASN* 4.1 23.8 - - + +
56C THR* 4.6 4.0 - - - +
63C ILE* 3.9 25.4 - - + -
101C LEU* 3.6 15.2 - - + +
102C GLN* 3.5 4.2 + - - -
103C ALA* 2.7 49.2 + - + +
113C VAL* 5.3 6.5 - - + -
144C ILE* 5.6 0.2 - - + -
145C CYS* 4.6 16.6 - - + -
147C LEU* 4.9 5.6 - - + -
152C GLU* 1.3 76.0 - - - +
154C LYS* 1.3 63.5 + - - +
155C LEU* 4.0 34.1 - - + -
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Residues in contact with LYS 154 (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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52C GLU* 2.9 73.8 + - + +
53C THR* 2.9 19.0 + - - +
100C THR* 5.3 3.6 - - + -
101C LEU 3.4 1.8 - - - +
102C GLN* 3.4 42.5 + - + +
103C ALA 5.2 0.7 - - - +
152C GLU* 5.0 17.5 - - + -
153C LEU* 1.3 75.3 - - - +
155C LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 155 (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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49C VAL* 4.1 6.7 - - + -
50C GLU 3.7 3.6 - - - +
51C VAL* 3.4 45.8 - - + -
52C GLU* 5.8 0.7 - - - -
63C ILE* 4.2 17.5 - - + -
64C ALA 6.4 0.2 - - - +
67C LEU* 3.6 27.8 - - + -
100C THR* 3.2 26.7 - - - +
101C LEU* 2.9 43.3 + - + -
153C LEU* 4.0 17.9 - - + -
154C LYS* 1.3 76.9 - - - +
156C THR* 1.3 65.4 + - - +
157C CYS* 4.9 4.3 - - - -
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Residues in contact with THR 156 (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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48C SER 3.7 0.9 - - - +
49C VAL* 3.3 4.5 - - - +
50C GLU* 2.8 68.9 + - + +
52C GLU* 5.5 5.4 + - - +
98C VAL* 4.1 21.3 - - + -
99C LEU 3.5 3.1 - - - +
100C THR* 4.7 4.0 + - - +
155C LEU* 1.3 74.9 + - - +
157C CYS* 1.3 64.1 + - - +
158C VAL* 4.1 6.5 + - + +
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Residues in contact with CYS 157 (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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46C ILE* 3.6 32.1 - - + -
48C SER 3.3 4.0 - - - -
49C VAL* 4.6 2.0 - - - -
67C LEU* 3.7 29.6 - - - -
97C VAL 3.8 0.9 - - - +
98C VAL* 3.2 3.4 - - - +
99C LEU* 2.5 51.5 + - + +
101C LEU* 5.6 0.7 - - - -
118C LEU* 4.4 17.9 - - - -
155C LEU* 4.9 7.9 - - - -
156C THR* 1.3 76.4 - - - +
158C VAL* 1.3 62.3 + - - +
159C ALA 4.1 0.2 - - - -
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Residues in contact with VAL 158 (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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46C ILE* 4.5 1.3 - - - -
47C ASP* 2.9 7.1 + - - +
48C SER* 2.8 52.6 + - - +
91C HIS* 3.4 41.5 - - + +
96C SER* 3.5 31.9 - - - +
97C VAL 3.7 3.6 - - - +
98C VAL* 4.0 14.6 - - + -
156C THR* 5.1 7.0 - - + +
157C CYS* 1.3 73.3 - - - +
159C ALA* 1.3 61.7 + - - +
160C LYS* 3.9 11.1 - - - +
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Residues in contact with ALA 159 (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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44C LEU* 3.7 21.5 - - + +
45C ALA 3.6 9.0 - - - +
46C ILE* 3.9 6.5 - - + +
72C LEU* 3.5 31.6 - - + -
96C SER* 3.3 24.1 - - - -
97C VAL* 3.0 20.8 + - + +
99C LEU* 5.4 1.1 - - + -
157C CYS 4.1 1.2 - - - -
158C VAL* 1.3 72.6 - - - +
160C LYS* 1.3 60.6 + - - +
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Residues in contact with LYS 160 (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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44C LEU* 3.2 17.6 - - - +
45C ALA 3.3 10.6 + - - -
47C ASP* 4.0 29.7 + - + +
48C SER* 4.5 14.6 - - - -
83C SER* 3.6 31.1 + - - +
90C ASP* 3.3 35.4 + - - -
91C HIS* 4.4 4.9 + - - -
95C CYS 4.6 4.3 - - - -
96C SER* 4.6 0.4 - - - -
158C VAL* 3.9 23.3 + - + +
159C ALA* 1.3 78.6 - - - +
161C LYS* 1.3 64.5 + - - +
170C TRP* 3.3 21.7 + - + -
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Residues in contact with LYS 161 (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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42C PRO* 3.9 21.2 - - + +
43C THR 3.7 3.8 - - - -
44C LEU* 4.2 3.3 - - - +
77C ILE* 3.6 34.9 + - + -
78C GLU* 4.0 19.4 + - - +
80C LEU* 3.4 28.4 + - + +
81C GLU 4.2 4.5 - - - +
82C TYR* 3.6 64.5 - - + +
83C SER 5.1 3.4 + - - +
84C ARG* 5.0 1.4 + - - -
95C CYS 4.8 3.6 + - - -
160C LYS* 1.3 78.1 - - - +
162C GLY* 1.3 61.9 + - - +
166C GLU* 4.8 2.8 - - - +
170C TRP* 4.1 7.9 - - - -
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Residues in contact with GLY 162 (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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42C PRO* 3.4 6.6 - - - +
43C THR 3.3 29.2 + - - -
82C TYR* 4.7 4.3 - - - -
84C ARG* 5.8 0.2 - - - -
161C LYS* 1.3 78.4 - - - +
163C ILE* 1.3 65.0 + - - -
166C GLU* 4.5 4.7 - - - -
170C TRP* 3.3 30.9 - - - +
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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