Contacts of the strand formed by residues 162 - 170 (chain C) in PDB entry 3SKU
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 GLY 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.7 16.6 - - - -
160C THR 3.1 8.1 + - - -
161C ALA* 1.3 73.1 - - - +
163C THR* 1.3 62.1 + - - -
164C TYR* 3.8 4.3 - - - -
180C ILE* 3.8 5.7 - - - +
181C LEU 3.3 29.8 + - - +
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Residues in contact with THR 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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101C ARG* 3.8 2.9 - - - +
102C MET* 2.9 45.5 + - + +
162C GLY* 1.3 72.3 - - - -
164C TYR* 1.3 79.4 - - - +
165C LEU* 5.0 0.7 - - + -
178C GLN* 4.0 22.9 - - + +
179C PHE 3.7 6.1 - - - +
180C ILE* 4.3 19.5 - - + +
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Residues in contact with TYR 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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71C LEU* 3.7 21.8 - - + -
99C TRP* 4.2 5.2 - + + -
100C PHE 3.5 4.7 - - - -
101C ARG* 3.6 19.4 + - - -
102C MET* 4.4 0.7 - - - -
110C ILE* 3.9 16.6 - - + -
138C TYR* 2.8 38.2 + + - -
151C PHE* 4.8 3.4 - + - -
153C MET* 3.6 23.8 - - + -
160C THR* 2.8 41.1 + - - -
162C GLY 3.8 12.8 - - - -
163C THR* 1.3 92.3 - - - +
165C LEU* 1.3 69.8 + - - +
179C PHE* 2.8 42.0 + - - +
181C LEU* 4.7 8.3 - - + -
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Residues in contact with LEU 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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47C PRO* 4.3 23.6 - - + +
55C ILE* 5.8 0.9 - - + -
98C ALA 3.5 4.5 - - - +
99C TRP* 3.5 6.9 - - - -
100C PHE* 3.0 37.9 + - + +
102C MET* 3.9 36.3 - - + -
163C THR* 5.0 0.9 - - + -
164C TYR* 1.3 82.6 - - - +
166C ARG* 1.3 60.8 - - - +
176C ILE* 3.3 31.9 - - + -
177C THR 3.4 13.0 - - - +
178C GLN* 3.8 23.3 - - + +
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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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72C ASN* 4.8 0.2 + - - -
73C ALA* 3.4 31.2 + - - +
74C PRO 4.3 2.4 + - - -
75C SER* 3.3 19.2 + - - +
97C ILE* 4.8 3.1 - - + -
98C ALA 3.4 5.2 - - - +
99C TRP* 3.5 36.0 - - + +
100C PHE* 5.3 0.4 - - - -
149C LEU* 3.2 40.7 + - - +
165C LEU* 1.3 75.4 - - - +
167C LEU* 1.3 69.7 + - - +
168C VAL* 3.9 14.3 - - - +
175C GLU* 2.7 28.9 + - - -
176C ILE* 3.7 13.9 - - - +
177C THR* 2.8 46.6 + - - +
179C PHE* 4.1 7.6 - - + -
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Residues in contact with LEU 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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45C PRO* 3.4 39.9 - - + -
46C ASP 4.4 15.0 - - - +
47C PRO* 4.8 3.6 - - + -
96C THR 4.0 1.1 - - - +
97C ILE* 3.0 10.4 - - - +
98C ALA* 2.7 47.3 + - + +
100C PHE* 4.4 9.2 - - + -
166C ARG* 1.3 76.5 - - - +
168C VAL* 1.3 89.0 + - - +
169C LYS* 3.8 8.3 - - + +
174C THR* 3.4 31.6 - - + -
175C GLU 4.0 4.0 - - - +
176C ILE* 4.8 7.9 - - + -
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Residues in contact with VAL 168 (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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75C SER* 4.0 4.0 - - - +
77C ALA* 3.4 28.9 - - + -
95C LEU* 3.7 19.3 - - + -
96C THR 3.4 2.2 - - - -
97C ILE* 4.2 9.0 - - + -
124C LEU* 5.0 0.4 - - + -
149C LEU* 3.8 25.6 - - + -
166C ARG* 3.9 18.6 - - - +
167C LEU* 1.3 81.8 - - - +
169C LYS* 1.3 61.8 + - - +
170C ILE* 4.2 1.6 - - + -
173C TRP* 3.7 8.0 - - + -
174C THR* 3.6 2.1 - - - -
175C GLU* 3.0 41.7 + - + +
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Residues in contact with LYS 169 (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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41C GLN* 4.9 14.2 + - - +
45C PRO* 4.6 20.1 - - + +
49C GLN* 5.8 4.9 - - - +
94C ASN 3.3 4.7 - - - +
95C LEU* 3.4 0.4 - - - -
96C THR* 2.8 49.3 + - - +
167C LEU* 3.8 15.2 - - + +
168C VAL* 1.3 74.8 - - - +
170C ILE* 1.3 59.9 + - - +
171C ASN* 2.9 27.3 + - - +
172C ASP* 4.9 2.2 + - - +
173C TRP 3.0 16.4 - - - +
174C THR* 3.8 13.5 - - + +
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Residues in contact with ILE 170 (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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77C ALA* 4.4 19.5 - - + +
80C ILE* 4.8 11.4 - - + -
81C VAL* 3.7 27.4 - - + -
93C TYR* 4.0 29.8 - - + -
94C ASN 3.3 2.7 - - - -
95C LEU* 3.5 24.7 - - + -
120C TYR* 5.7 1.8 - - + +
124C LEU* 3.9 16.8 - - + -
168C VAL* 4.2 1.5 - - + -
169C LYS* 1.3 69.4 - - - +
171C ASN* 1.3 61.8 + - + +
172C ASP 2.7 18.4 + - - -
173C TRP* 2.9 33.8 + - + +
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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