Contacts of the strand formed by residues 178 - 184 (chain C) in PDB entry 5NVN
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 178 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLY* 5.4 4.2 - - - -
138C ARG* 3.5 0.9 - - - -
139C LEU* 2.8 43.1 + - + +
140C ARG 4.4 0.2 - - - +
141C LYS* 2.8 45.6 + - - +
142C GLY 4.3 2.3 + - - -
144C ALA* 3.3 37.0 + - + +
171C VAL* 5.3 0.2 - - + -
172C SER 3.3 8.3 - - - +
173C VAL* 3.2 22.3 - - - +
177C GLU* 1.3 73.8 - - - +
179C ILE* 1.3 69.0 + - - +
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Residues in contact with ILE 179 (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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136C ILE* 4.3 27.8 - - + -
137C ILE 3.4 11.4 - - - +
138C ARG* 4.5 13.7 - - + +
139C LEU* 5.7 0.4 - - - -
170C VAL 4.0 0.2 - - - +
171C VAL* 3.3 4.3 - - - +
172C SER* 2.7 53.5 + - - +
174C ARG* 5.0 14.8 - - + +
177C GLU* 4.2 20.6 - - + +
178C ASP* 1.3 81.2 - - - +
180C ILE* 1.3 65.0 + - - +
181C SER* 5.3 2.2 - - - -
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Residues in contact with ILE 180 (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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136C ILE* 3.4 1.1 - - - -
137C ILE* 2.8 59.5 + - + +
139C LEU* 4.0 18.4 - - + +
144C ALA* 5.1 0.9 - - - +
147C CYS* 3.7 10.1 - - + +
148C TRP* 3.5 42.4 - - + +
151C LEU* 3.4 28.9 - - + -
170C VAL 3.3 12.3 - - - +
171C VAL* 4.7 5.4 - - + -
179C ILE* 1.3 75.4 - - - +
181C SER* 1.3 64.0 + - - +
204C LEU* 4.7 7.9 - - + -
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Residues in contact with SER 181 (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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134C LYS* 4.2 10.0 + - - +
135C TRP 2.9 18.2 - - - -
136C ILE* 3.7 17.3 - - - -
137C ILE* 5.6 1.1 - - - -
151C LEU* 3.8 5.9 - - - +
169C ALA* 3.3 5.9 - - - +
170C VAL* 2.9 42.9 + - - +
179C ILE* 5.3 3.1 - - - -
180C ILE* 1.3 75.9 - - - +
182C ILE* 1.3 59.1 + - - +
183C TRP* 3.5 18.3 + - - -
200C LEU* 6.2 0.2 - - - -
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Residues in contact with ILE 182 (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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134C LYS* 3.2 1.6 - - - -
135C TRP* 3.0 25.3 + - + -
151C LEU* 4.2 12.8 - - + -
155C MET* 4.6 6.3 - - - -
160C PHE* 3.5 37.2 - - + -
166C ILE* 3.8 25.8 - - + -
168C GLY 3.4 14.4 - - - +
169C ALA* 4.9 0.7 - - + -
181C SER* 1.3 74.3 - - - +
183C TRP* 1.3 72.1 + - - +
184C ASN* 4.1 1.9 + - - +
196C ILE* 3.7 24.3 - - + +
200C LEU* 3.9 22.4 - - + -
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Residues in contact with TRP 183 (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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114C HIS* 5.9 0.7 - + - -
116C PHE* 3.5 23.8 - + + -
122C PRO 3.8 20.4 - - - -
123C MET* 3.8 17.0 - - - -
124C TRP* 4.0 4.3 - - + -
129C ASN* 3.6 24.2 - - - -
133C GLY 3.3 7.0 - - - +
134C LYS* 3.5 29.9 - - + +
166C ILE* 3.7 6.1 - - - +
167C CYS* 2.8 34.4 + - + -
168C GLY 2.8 16.0 + - - +
170C VAL* 3.7 16.1 - - + +
181C SER* 3.5 19.7 + - - -
182C ILE* 1.3 79.2 - - - +
184C ASN* 1.3 61.4 + - - +
217C HIS* 3.2 35.2 - + + -
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Residues in contact with ASN 184 (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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129C ASN* 5.1 0.3 - - - +
132C GLY* 3.3 2.9 - - - -
133C GLY 3.0 27.3 + - - +
134C LYS* 4.5 0.5 - - - -
135C TRP* 5.5 0.2 - - - -
165C GLU* 3.0 27.6 + - + +
166C ILE* 4.6 0.2 - - - -
167C CYS* 3.7 6.9 - - - -
182C ILE 4.8 1.0 - - - +
183C TRP* 1.3 75.5 - - - +
185C LYS* 1.3 61.7 + - - +
186C THR 2.9 29.3 + - - -
192C THR* 3.9 10.1 - - - +
193C THR* 3.9 4.6 - - - +
196C ILE* 3.5 27.4 - - + +
214C TYR* 2.7 33.8 + - - -
217C HIS* 4.6 2.3 + - - -
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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