Contacts of the helix formed by residues 144 - 156 (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 ALA 144 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C PRO* 4.4 7.9 - - + -
105C GLY* 4.8 5.4 - - - +
139C LEU* 4.5 11.4 - - + +
140C ARG 4.9 0.4 + - - -
142C GLY 3.7 0.8 - - - -
143C LEU* 1.3 78.5 - - - +
145C SER* 1.3 58.8 + - - +
147C CYS* 4.6 0.4 - - - -
148C TRP* 2.8 35.7 + - - +
171C VAL* 4.0 18.6 - - + +
173C VAL* 5.0 0.9 - - + -
178C ASP* 3.3 38.3 + - + +
180C ILE* 5.1 1.1 - - + +
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TYR* 4.4 1.4 + - - -
103C ARG* 3.4 39.9 + - - +
104C PRO* 4.0 11.3 - - - +
105C GLY* 2.8 31.6 + - - +
106C ASP* 5.3 0.2 + - - -
142C GLY 5.3 3.1 + - - -
143C LEU 3.4 0.6 - - - -
144C ALA* 1.3 77.9 - - - +
146C ARG* 1.3 62.2 + - - +
148C TRP* 3.7 2.3 - - - +
149C GLU* 3.1 23.2 + - - +
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Residues in contact with ARG 146 (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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103C ARG* 4.9 4.3 - - - +
142C GLY 5.5 2.4 + - - +
143C LEU* 3.3 11.0 + - + +
144C ALA 3.3 0.2 - - - -
145C SER* 1.3 79.3 - - - +
147C CYS* 1.3 65.6 + - - +
149C GLU* 3.4 12.7 + - - +
150C ASN* 3.0 30.4 + - - +
305C FMT 2.4 39.4 + - - -
56D ARG* 3.5 17.0 - - - +
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Residues in contact with CYS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 3.5 33.7 - - + -
143C LEU* 3.0 28.0 + - - +
144C ALA 4.0 1.1 - - - +
146C ARG* 1.3 75.9 - - - +
148C TRP* 1.3 61.7 + - - +
150C ASN* 3.1 8.3 + - - +
151C LEU* 2.8 31.2 + - - +
180C ILE* 3.7 12.3 - - + -
204C LEU* 3.5 25.7 - - + +
206C LEU* 5.4 3.8 - - - -
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Residues in contact with TRP 148 (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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62C PHE* 4.2 18.7 - + - -
98C TYR* 4.2 12.7 - + - -
101C MET* 5.9 0.6 - - - +
104C PRO* 3.3 30.7 - - + +
113C PHE* 3.9 29.4 - - + -
115C LEU* 3.9 10.3 - - + -
144C ALA 2.8 22.4 + - - +
145C SER 3.7 2.5 - - - +
147C CYS* 1.3 72.9 - - - +
149C GLU* 1.3 63.6 + - - +
151C LEU* 3.2 2.1 + - + +
152C ILE* 3.0 61.5 + - + +
169C ALA* 3.6 27.8 - - + -
170C VAL 3.5 27.6 - - - -
171C VAL* 3.5 20.9 - - + -
180C ILE* 3.5 19.3 - - + +
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Residues in contact with GLU 149 (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 PHE* 6.2 0.4 - - + -
95C TRP* 4.7 4.5 - - + -
98C TYR* 2.8 42.0 + - + +
103C ARG* 3.2 22.7 + - - +
145C SER 3.1 11.2 + - - +
146C ARG* 3.7 11.8 - - - +
148C TRP* 1.3 78.5 - - - +
150C ASN* 1.3 63.7 + - - +
152C ILE* 3.4 8.2 - - + +
153C LEU* 3.1 45.3 + - + +
56D ARG* 3.8 18.6 + - - +
60D MET* 4.0 14.9 - - - +
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Residues in contact with ASN 150 (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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146C ARG* 3.0 30.2 + - - +
147C CYS* 3.1 9.7 + - - +
149C GLU* 1.3 75.5 - - - +
151C LEU* 1.3 63.3 + - - +
153C LEU* 4.0 2.5 - - - +
154C ALA* 3.1 23.0 + - - +
203C VAL* 3.6 20.4 + - - +
204C LEU* 3.8 14.0 + - + +
205C ASN* 3.9 3.8 + - - -
305C FMT 3.1 26.2 + - - -
56D ARG* 2.8 40.9 + - - +
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Residues in contact with LEU 151 (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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137C ILE* 6.4 0.4 - - + -
147C CYS 2.8 20.1 + - - +
148C TRP* 3.2 4.9 + - + +
150C ASN* 1.3 74.0 - - - +
152C ILE* 1.3 58.9 + - + +
154C ALA* 3.0 6.0 + - + +
155C MET* 2.8 27.6 + - + +
160C PHE* 3.7 26.7 - - + -
169C ALA* 3.7 27.1 - - + -
180C ILE* 3.4 32.5 - - + -
181C SER 3.8 12.3 - - - +
182C ILE* 4.2 9.2 - - + -
200C LEU* 3.7 20.6 - - + -
203C VAL* 5.0 1.1 - - + -
204C LEU* 3.7 9.8 - - + +
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Residues in contact with ILE 152 (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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62C PHE* 4.6 3.4 - - + -
94C PHE* 3.8 30.3 - - + -
98C TYR* 3.9 17.7 - - + -
115C LEU* 3.7 21.1 - - + -
148C TRP* 3.0 73.9 + - + +
149C GLU* 3.4 8.1 - - + +
151C LEU* 1.3 76.0 - - - +
153C LEU* 1.3 56.0 + - - +
155C MET* 3.8 11.8 - - + +
156C LEU* 2.7 41.8 + - - +
169C ALA* 4.5 2.0 - - + -
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Residues in contact with LEU 153 (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 PHE* 3.6 32.8 - - + -
95C TRP* 3.8 13.0 - - + -
149C GLU* 3.1 34.5 + - + +
150C ASN 4.0 2.9 - - - +
152C ILE* 1.3 79.4 - - + +
154C ALA* 1.3 56.1 + - - +
156C LEU* 4.5 2.7 - - + -
157C GLY* 2.8 25.3 + - - -
159C GLN* 4.9 0.2 - - - +
54D TYR 4.8 0.9 - - - +
56D ARG* 4.2 19.7 - - + +
59D LEU* 3.3 30.7 - - + +
60D MET* 3.3 39.7 - - + -
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Residues in contact with ALA 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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150C ASN 3.1 15.3 + - - +
151C LEU 3.0 9.7 + - - +
153C LEU* 1.3 74.5 - - - +
155C MET* 1.3 62.7 + - - +
157C GLY 3.4 0.5 + - - -
158C GLU 3.2 3.6 + - - -
159C GLN* 2.9 42.6 + - + +
160C PHE* 3.9 9.1 - - + -
203C VAL* 3.7 35.7 - - + -
56D ARG* 6.5 0.4 - - - -
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Residues in contact with MET 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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60C TYR* 3.7 28.6 + - + +
115C LEU* 3.5 45.5 - - + +
151C LEU* 2.8 18.9 + - + +
152C ILE* 3.8 6.7 - - + +
154C ALA* 1.3 70.1 - - - +
156C LEU* 1.3 67.2 + - - +
158C GLU* 3.1 17.0 + - - +
160C PHE* 3.6 18.2 - - + -
166C ILE* 3.8 30.7 - - + -
168C GLY* 3.8 18.8 - - - -
169C ALA* 3.8 17.5 - - + -
182C ILE* 4.6 4.3 - - + -
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Residues in contact with LEU 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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56C LEU* 3.7 30.3 - - + +
57C GLN* 5.1 2.4 + - - +
60C TYR* 3.3 49.1 - - + -
88C PHE* 4.0 12.6 - - + -
91C VAL* 6.4 0.2 - - - -
94C PHE* 3.3 52.3 - - + -
115C LEU* 4.2 8.1 - - + -
152C ILE 2.7 28.7 + - - +
153C LEU* 4.1 4.7 - - + +
155C MET* 1.3 73.9 - - + +
157C GLY* 1.3 56.2 + - - +
158C GLU* 3.2 12.1 + - - +
52D ILE 4.8 0.9 - - - +
54D TYR* 4.6 2.4 - - - -
59D LEU* 4.9 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