Contacts of the strand formed by residues 162 - 173 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLU 4.3 4.0 - - - +
22A ALA* 4.5 7.6 - - - -
23A ASP* 4.6 4.5 + - - +
143A GLU* 3.4 27.6 - - + +
144A PHE 3.5 8.1 - - - +
145A SER* 4.5 3.7 + - - +
160A LYS* 3.5 11.0 - - + +
161A MET* 1.3 76.0 - - - +
163A THR* 1.3 66.8 + - - +
164A LYS* 3.2 39.8 - - + +
96D ASP* 2.9 16.3 + - - +
101D VAL* 6.3 5.2 - - + -
119D LYS* 3.8 21.7 - - - +
121D ASP* 5.2 1.2 + - - -
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Residues in contact with THR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.6 3.4 - - + -
21A GLU 3.5 12.1 - - - +
22A ALA* 4.8 7.4 - - + +
143A GLU* 3.3 3.7 - - - -
144A PHE* 2.7 65.5 + - + -
146A ARG* 3.8 19.4 + - - +
161A MET 3.0 13.7 + - - -
162A LYS* 1.3 74.9 + - - +
164A LYS* 1.3 68.5 + - - +
165A LEU* 5.1 0.2 - - + -
201A OTP 4.0 24.9 - - + -
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.1 10.4 - - - +
21A GLU* 2.9 61.6 + - + +
142A GLY 3.5 4.9 - - - +
143A GLU* 3.6 22.1 + - + +
162A LYS* 3.2 38.7 - - + +
163A THR* 1.3 75.6 - - - +
165A LEU* 1.3 62.3 + - - +
166A LEU* 4.3 8.3 - - + -
119D LYS* 4.4 7.5 - - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO* 4.9 4.3 - - + -
19A SER 3.4 11.7 - - - +
20A PHE* 4.3 7.0 - - + -
116A LEU* 4.0 25.8 - - + -
118A LEU* 4.7 7.6 - - + -
141A VAL* 3.2 7.7 - - - +
142A GLY 2.8 38.3 + - - +
144A PHE* 3.8 27.4 - - + -
163A THR* 5.1 0.2 - - + -
164A LYS* 1.3 78.9 - - - +
166A LEU* 1.3 64.9 + - - +
167A ILE* 4.1 14.4 - - + -
201A OTP 4.0 47.8 - - + -
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR 3.9 1.0 - - - +
19A SER* 2.8 43.6 + - - +
20A PHE 4.4 2.9 - - - -
21A GLU* 3.9 38.4 - - + +
140A ALA 3.6 4.9 - - - +
141A VAL* 4.8 10.5 - - + -
164A LYS* 4.2 13.0 - - + +
165A LEU* 1.3 79.2 - - - +
167A ILE* 1.3 61.3 + - - +
168A THR* 4.9 0.2 + - - -
21B GLU* 4.4 7.4 - - - +
32B ARG* 3.8 42.3 + - - +
166B LEU* 5.7 2.9 - - + -
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR 3.7 2.7 - - - +
18A PRO* 4.3 14.8 - - + -
118A LEU* 3.7 39.3 - - + -
138A VAL* 3.8 1.0 - - + +
139A ASP* 3.1 12.5 - - - +
140A ALA* 2.8 46.7 + - + +
141A VAL 5.3 0.2 - - - -
165A LEU* 4.3 17.7 - - + -
166A LEU* 1.3 75.8 - - - +
168A THR* 1.3 68.2 + - - +
169A ALA* 4.5 2.5 - - + -
201A OTP 3.5 50.7 - - + -
32B ARG* 4.3 0.6 - - - +
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 3.4 23.3 - - + +
16A THR* 3.3 1.2 - - - +
17A TYR* 2.9 45.7 + - + +
19A SER* 5.1 1.4 + - - -
34A LYS* 5.7 0.9 + - - -
138A VAL 3.9 3.4 - - - -
139A ASP* 4.4 2.5 - - - -
166A LEU 4.9 0.5 + - - -
167A ILE* 1.3 75.4 - - - +
169A ALA* 1.3 65.5 + - - +
29B SER* 3.8 18.6 - - - +
30B VAL 2.7 29.7 + - - +
31B TRP* 5.4 2.0 - - + -
32B ARG* 3.5 18.4 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.7 25.4 - - + -
15A HIS 3.4 4.3 - - - -
16A THR* 3.7 9.0 - - + -
137A GLY* 3.2 3.1 - - - -
138A VAL* 2.8 52.5 + - + +
167A ILE* 4.1 0.6 - - + -
168A THR* 1.3 78.8 - - - +
170A GLU* 1.3 65.6 + - - +
201A OTP 4.0 14.7 - - + +
29B SER* 4.3 0.3 - - - -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.5 3.4 - - - -
12A ASP* 2.9 31.7 + - + +
15A HIS* 3.3 29.9 + - + +
16A THR* 3.3 5.3 + - - -
128A HIS* 5.2 4.0 + - - -
135A VAL* 4.1 10.7 - - + +
136A CYS 3.3 5.8 - - - +
137A GLY* 4.3 0.2 - - - -
169A ALA* 1.3 81.2 - - - +
171A ALA* 1.3 61.7 + - - +
24B HIS* 2.7 32.8 + - - -
25B PHE* 4.9 1.0 - - - -
28B LEU* 3.3 27.3 - - + +
29B SER* 2.5 31.7 + - - +
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.5 27.1 - - + -
10A GLN 3.3 15.0 - - - +
11A PHE* 3.9 16.8 - - + -
42A VAL* 4.3 5.4 - - + -
135A VAL* 3.4 2.1 - - - -
136A CYS* 2.8 33.9 + - + +
170A GLU* 1.3 76.6 - - - +
172A VAL* 1.3 63.2 + - - +
201A OTP 4.3 8.2 - - + +
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.8 2.0 - - - -
10A GLN* 2.9 37.9 + - + +
12A ASP* 4.5 17.3 - - + -
128A HIS* 4.3 5.8 - - + -
131A LEU* 3.8 30.3 - - + -
133A ARG* 3.7 37.7 + - + +
134A GLU 3.5 10.3 - - - +
135A VAL* 4.2 14.1 - - + +
171A ALA* 1.3 75.6 - - - +
173A LYS* 1.3 69.6 + - - +
174A GLN* 3.4 1.4 + - - -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 4.1 18.8 - - + +
8A THR 3.5 11.2 - - - +
9A TYR* 3.4 22.2 + - + -
133A ARG* 2.8 28.3 + - + +
134A GLU* 2.8 52.9 + - + +
172A VAL* 1.3 72.3 - - - +
174A GLN* 1.3 71.8 + - - +
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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