Contacts of the strand formed by residues 162 - 173 (chain C) in PDB entry 5IXG
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 LYS 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ASP* 3.0 18.0 + - - +
101B VAL* 6.3 3.1 - - + -
119B LYS* 4.4 19.3 - - + +
21C GLU 4.2 4.2 - - - +
22C ALA* 4.6 6.8 - - - -
23C ASP* 4.6 3.3 + - - +
143C GLU* 3.1 36.6 + - + +
144C PHE 3.6 7.9 - - - +
145C SER* 4.5 4.2 + - - +
160C LYS* 3.4 13.3 - - + +
161C MET* 1.3 75.7 - - - +
163C THR* 1.3 64.5 + - - +
164C LYS* 4.3 7.8 + - - +
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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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20C PHE* 4.5 4.3 - - + -
21C GLU 3.5 11.7 - - - +
22C ALA* 4.8 6.3 - - + +
143C GLU* 3.3 3.6 - - - -
144C PHE* 2.7 62.6 + - + -
146C ARG* 3.7 20.3 + - - +
161C MET 3.0 13.5 + - - -
162C LYS* 1.3 76.5 + - - +
164C LYS* 1.3 68.4 + - - +
165C LEU* 3.9 0.8 + - + -
201C OTP 4.1 23.3 - - + -
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Residues in contact with LYS 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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20C PHE* 3.1 10.2 - - - +
21C GLU* 2.9 62.7 + - + +
141C VAL* 4.4 17.9 - - - +
142C GLY 3.6 11.0 - - - +
143C GLU* 4.4 15.7 - - + +
162C LYS* 4.2 7.9 + - - +
163C THR* 1.3 72.9 - - - +
165C LEU* 1.3 63.9 + - - +
166C LEU* 3.8 31.5 - - + +
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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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18C PRO* 5.1 1.1 - - + -
19C SER 3.4 11.0 - - - +
20C PHE* 4.3 7.0 - - + -
107C LEU* 5.0 0.7 - - + -
116C LEU* 4.0 25.4 - - + -
118C LEU* 4.6 7.2 - - + -
141C VAL* 3.2 7.7 - - - +
142C GLY 2.8 41.4 + - - +
144C PHE* 3.8 28.3 - - + -
163C THR* 5.1 0.2 - - + -
164C LYS* 1.3 80.0 - - - +
166C LEU* 1.4 64.2 + - - +
167C ILE* 4.0 16.4 - - + -
201C OTP 4.0 48.0 - - + -
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Residues in contact with LEU 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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17C TYR 3.9 0.7 - - - +
19C SER* 2.8 44.7 + - - +
20C PHE* 4.4 3.4 - - - -
21C GLU* 3.9 27.8 - - + +
140C ALA 3.6 4.3 - - - +
141C VAL* 4.5 5.8 - - + -
164C LYS* 3.8 44.6 - - + +
165C LEU* 1.4 78.1 - - - +
167C ILE* 1.3 61.5 + - - +
168C THR 4.0 0.3 + - - -
21D GLU* 4.4 8.1 - - - +
32D ARG* 3.8 41.5 + - - +
166D LEU* 5.9 2.2 - - + -
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Residues in contact with ILE 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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17C TYR 3.8 1.8 - - - +
18C PRO* 3.7 28.3 - - + -
118C LEU* 4.3 21.3 - - + -
138C VAL* 3.7 1.3 - - + +
139C ASP* 3.0 12.6 - - - +
140C ALA* 2.8 47.1 + - + +
165C LEU* 4.0 23.1 - - + -
166C LEU* 1.3 75.0 - - - +
168C THR* 1.3 65.7 + - - +
169C ALA* 4.4 2.0 - - + +
201C OTP 3.6 57.0 - - + -
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Residues in contact with THR 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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15C HIS* 3.4 20.2 - - + +
16C THR* 3.3 1.4 - - - +
17C TYR* 2.9 45.4 + - + +
19C SER* 5.2 1.6 + - - -
34C LYS* 5.7 1.0 + - - -
138C VAL 3.8 3.6 - - - -
139C ASP* 4.3 2.7 - - - -
166C LEU 4.0 0.7 + - - -
167C ILE* 1.3 73.0 - - - +
169C ALA* 1.3 67.1 + - - +
29D SER* 3.7 19.5 - - - +
30D VAL 2.7 30.1 + - - +
31D TRP* 4.9 3.6 - - + +
32D ARG* 3.5 17.2 + - - +
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Residues in contact with ALA 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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11C PHE* 3.8 24.0 - - + -
15C HIS 3.5 3.6 - - - -
16C THR* 3.7 9.9 - - + -
137C GLY* 3.3 2.9 - - - -
138C VAL* 2.9 53.3 + - + +
167C ILE* 4.4 0.7 - - + -
168C THR* 1.3 79.6 - - - +
170C GLU* 1.3 64.7 + - - +
201C OTP 4.0 13.1 - - + +
29D SER* 4.3 0.7 - - - -
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Residues in contact with GLU 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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11C PHE* 3.5 3.0 - - - -
12C ASP* 2.8 30.2 + - + +
15C HIS* 3.3 26.2 + - + +
16C THR* 3.2 11.0 + - - -
128C HIS* 5.6 2.4 - - - -
135C VAL* 4.2 10.6 - - + +
136C CYS 3.3 7.6 - - - +
137C GLY* 4.3 5.8 - - - -
169C ALA* 1.3 78.6 - - - +
171C ALA* 1.3 60.5 + - - +
24D HIS* 2.6 36.6 + - - -
28D LEU* 3.6 20.5 - - + +
29D SER* 2.4 32.5 + - - +
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Residues in contact with ALA 171 (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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9C TYR* 3.5 26.0 - - + -
10C GLN 3.4 11.4 - - - +
11C PHE* 3.9 11.0 - - + -
12C ASP 4.2 0.7 - - - +
42C VAL* 3.8 17.9 - - + -
135C VAL* 3.2 4.4 - - - -
136C CYS* 2.8 31.9 + - + +
170C GLU* 1.3 76.1 - - - +
172C VAL* 1.3 64.0 + - - +
201C OTP 4.2 6.3 - - + -
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Residues in contact with VAL 172 (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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9C TYR* 3.7 2.0 - - - -
10C GLN 2.9 25.7 + - - +
12C ASP* 4.4 20.4 - - + +
131C LEU* 4.5 19.7 - - + -
133C ARG* 3.5 45.3 - - + +
134C GLU 3.6 9.4 - - - +
135C VAL* 4.5 11.9 - - + -
171C ALA* 1.3 77.1 - - - +
173C LYS* 1.4 63.6 + - - +
174C GLN* 2.9 20.9 - - - +
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Residues in contact with LYS 173 (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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6C SER 4.9 4.9 + - - +
7C ALA* 3.6 31.5 - - + +
8C THR 3.6 0.9 - - - +
9C TYR* 3.4 16.9 + - + -
133C ARG* 3.0 27.2 + - + -
134C GLU* 3.0 54.4 + - + +
172C VAL* 1.4 70.3 - - - +
174C GLN* 1.3 71.3 + - - +
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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