Contacts of the strand formed by residues 159 - 167 (chain C) in PDB entry 2IVF
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 GLU 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C LYS* 3.2 32.7 + - + +
75C TRP 3.1 17.7 - - - +
76C ALA* 4.2 5.7 - - + +
155C HIS* 3.2 9.8 + - - -
156C ARG 2.9 33.8 + - - +
157C ASN* 4.2 7.6 - - - +
158C GLY* 1.3 83.2 - - - +
160C TRP* 1.3 66.8 + - - +
161C ASN* 3.5 8.6 + - - +
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Residues in contact with TRP 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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73C LEU 4.3 0.4 - - - -
74C LYS* 3.1 29.3 - - - +
75C TRP* 2.9 56.6 + + + -
77C SER* 3.9 7.2 - - - -
79C LYS* 3.8 22.2 - - + -
81C ASP* 4.0 10.3 - - + -
91C ASP* 2.7 28.5 + - + -
120C TRP* 3.7 24.7 - + - -
122C ALA* 3.7 28.5 - - + -
153C ALA* 4.0 9.6 - - + -
154C GLN* 3.6 23.1 - - - -
155C HIS* 3.6 37.5 - + + -
159C GLU* 1.3 72.3 - - - +
161C ASN* 1.3 61.5 + - - +
162C VAL* 4.1 1.8 - - + -
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Residues in contact with ASN 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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16C LEU* 3.6 9.1 - - + +
72C ARG* 3.3 25.7 - - - +
73C LEU 3.4 5.6 - - - +
74C LYS* 3.4 31.3 - - - +
153C ALA* 3.2 2.1 - - - -
154C GLN 2.8 41.9 + - - +
156C ARG* 2.9 39.4 + - - +
159C GLU* 3.5 17.4 + - - +
160C TRP* 1.3 76.1 - - - +
162C VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 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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16C LEU* 4.0 0.6 - - - +
71C LEU 3.6 0.7 - - - +
72C ARG* 3.4 2.6 - - - +
73C LEU* 2.8 49.3 + - + +
75C TRP* 3.4 33.9 - - + -
93C VAL* 4.2 11.4 - - + -
120C TRP* 4.0 31.4 - - + -
152C VAL 3.1 11.0 - - - +
153C ALA* 3.9 7.2 - - + -
160C TRP* 4.4 1.6 - - + -
161C ASN* 1.3 80.2 - - - +
163C ILE* 1.3 74.8 + - - +
164C LEU* 4.3 5.2 - - + -
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Residues in contact with ILE 163 (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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13C LEU 3.2 29.8 - - - +
14C LEU* 4.0 8.4 - - + +
16C LEU* 3.7 38.8 - - + +
21C TRP* 3.6 17.5 - - + +
70C ALA* 3.9 17.3 - - + -
71C LEU 3.1 9.4 - - - +
72C ARG* 3.8 16.4 - - + -
150C LYS 3.8 0.2 - - - +
151C ALA* 3.1 8.8 - - - +
152C VAL* 2.8 39.3 + - + +
162C VAL* 1.3 74.3 - - - +
164C LEU* 1.3 67.4 + - - +
165C CYS* 4.4 6.3 - - + +
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Residues in contact with LEU 164 (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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70C ALA* 3.4 1.4 - - - -
71C LEU* 2.8 37.7 + - + +
73C LEU* 4.1 17.7 - - + +
93C VAL* 4.5 13.7 - - + +
95C ALA* 4.7 9.2 - - + +
118C TRP* 3.6 57.2 - - + +
120C TRP* 4.1 10.1 - - + +
127C PRO* 3.8 29.8 - - + -
149C LEU* 4.6 1.8 - - + -
150C LYS 3.4 3.1 - - - +
151C ALA* 3.8 13.7 - - + -
162C VAL* 4.1 8.0 - - + -
163C ILE* 1.3 75.0 - - - +
165C CYS* 1.3 57.9 + - - +
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Residues in contact with CYS 165 (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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10C LYS* 5.0 2.0 - - - -
13C LEU* 4.9 5.4 - - - -
14C LEU* 3.7 37.0 - - + -
68C MET* 3.9 33.0 - - - -
69C ILE 3.4 9.9 - - - -
70C ALA* 4.2 13.7 - - + +
118C TRP* 5.0 0.2 - - - -
148C ASP 3.9 1.7 - - - +
149C LEU* 3.3 5.0 - - - +
150C LYS* 2.8 42.2 + - + +
163C ILE* 4.0 1.5 - - + -
164C LEU* 1.3 74.6 - - - +
166C ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 166 (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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68C MET* 4.2 5.6 - - - -
69C ILE* 2.8 37.0 + - - +
116C ASN* 4.3 2.2 - - - +
118C TRP* 3.6 28.7 - - + +
129C GLU* 3.9 15.7 - - - -
147C SER* 3.8 11.2 - - - +
148C ASP* 3.4 14.1 - - - +
149C LEU* 3.9 7.4 - - + +
165C CYS* 1.3 75.1 - - - +
167C SER* 1.3 76.5 + - - +
168C MET* 2.9 28.1 + - - +
170C THR* 3.2 25.7 + - + +
174C LEU* 4.4 1.4 - - - +
175C ALA* 2.9 42.0 + - - +
177C LEU* 3.6 26.3 - - - +
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Residues in contact with SER 167 (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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67C SER 3.3 11.9 + - - -
68C MET* 4.1 11.8 - - - +
69C ILE* 4.5 0.2 - - - +
148C ASP* 2.7 35.7 + - - -
166C ARG* 1.3 99.7 + - - +
168C MET* 1.3 64.4 + - - +
169C ALA* 3.8 16.2 - - - +
170C THR* 5.3 1.1 - - - -
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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