Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 1DS1
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 TYR 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.9 20.7 + + - -
54A ASN* 2.8 53.4 + - - -
105A LEU* 4.2 13.7 - - + -
154A PRO* 3.8 5.7 - - - +
155A ASN* 1.3 101.8 - - + +
157A VAL* 1.3 65.5 + - - +
158A MET* 4.1 1.3 - - + -
271A ILE* 4.0 21.3 - - + -
272A VAL 3.3 13.0 - - - +
273A ASP* 3.9 12.0 + - - -
274A ASN* 4.3 0.9 - - - -
299A TYR* 3.5 5.4 - - - -
300A ILE* 3.0 55.2 + - + +
302A THR* 3.6 13.0 - - + -
304A ARG* 3.2 8.5 + - - -
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Residues in contact with VAL 157 (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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146A GLU* 3.6 32.1 - - + -
154A PRO* 5.0 0.2 - - + -
156A TYR* 1.3 75.2 - - - +
158A MET* 1.3 63.1 + - - +
159A LEU* 4.3 16.2 - - + -
270A LEU 3.7 1.7 - - - +
271A ILE* 3.8 0.7 - - - -
272A VAL* 2.9 43.7 + - + +
274A ASN* 4.0 14.8 - - + +
279A HIS* 4.4 8.7 - - + +
297A ARG* 4.1 26.2 - - + -
298A VAL 3.8 2.5 - - - -
299A TYR* 4.0 13.9 - - + -
330A AKG 4.3 7.4 - - - +
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Residues in contact with MET 158 (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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98A LEU* 3.4 28.2 - - + +
101A VAL* 4.2 10.8 - - - -
102A GLY* 3.3 37.9 - - - +
105A LEU* 4.1 14.8 - - - -
156A TYR* 4.6 2.7 - - + -
157A VAL* 1.3 76.4 - - - +
159A LEU* 1.3 64.0 + - - +
160A ALA 4.2 0.4 - - - -
269A LEU* 4.3 4.0 - - + -
270A LEU 3.3 5.4 - - - +
271A ILE* 4.2 17.5 - - + -
296A HIS 3.6 0.7 - - - +
297A ARG* 3.3 7.4 - - - +
298A VAL* 3.0 55.1 + - + +
300A ILE* 3.8 17.5 - - + -
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Residues in contact with LEU 159 (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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123A VAL* 4.9 1.8 - - + -
157A VAL* 4.3 10.5 - - + +
158A MET* 1.3 79.9 - - - +
160A ALA* 1.3 60.0 + - - +
161A CYS 4.2 0.3 + - - -
172A THR* 4.5 13.2 - - + -
264A LEU* 4.3 16.2 - - + +
268A ASP 3.9 1.4 - - - +
269A LEU* 3.3 3.6 - - - -
270A LEU* 2.8 50.3 + - + +
272A VAL* 5.2 4.7 - - + -
279A HIS* 5.1 4.9 - - + -
295A LEU* 4.4 13.7 - - + -
296A HIS 3.4 2.9 - - - +
297A ARG* 3.8 19.5 - - + -
330A AKG 3.6 53.4 - - + +
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Residues in contact with ALA 160 (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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94A MET* 3.8 29.2 - - + +
98A LEU* 3.7 32.8 - - + -
158A MET 4.2 0.2 - - - -
159A LEU* 1.3 72.8 - - - +
161A CYS* 1.3 62.7 + - - +
268A ASP 3.4 4.9 - - - +
269A LEU* 4.1 4.3 - - + +
295A LEU* 3.2 6.6 - - - -
296A HIS* 2.8 35.6 + - + +
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Residues in contact with CYS 161 (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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94A MET* 3.7 9.5 - - - +
159A LEU 4.2 0.4 + - - -
160A ALA* 1.3 72.3 - - - +
162A SER* 1.4 57.1 + - - +
163A ARG 3.4 32.1 - - - -
164A ALA* 3.6 2.9 - - - -
264A LEU* 3.9 17.9 - - + -
265A GLU* 3.3 38.6 - - - +
266A PRO* 3.4 1.8 - - - +
267A GLY 3.0 23.2 + - - -
268A ASP 2.9 12.4 + - - +
295A LEU* 3.9 17.9 - - + -
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Residues in contact with SER 162 (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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70A VAL* 4.1 8.1 - - - +
71A GLU* 5.0 1.9 + - - +
73A ASP* 5.1 0.5 - - - +
76A LEU* 3.6 37.9 - - - +
92A LEU* 5.1 1.2 - - - +
94A MET* 3.9 11.8 + - - +
160A ALA 3.8 2.0 + - - -
161A CYS* 1.4 74.6 - - - +
163A ARG* 1.3 61.1 + - - +
266A PRO* 3.6 17.5 - - - +
294A TRP* 3.0 17.5 + - - -
296A HIS* 2.7 34.2 + - - -
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Residues in contact with ARG 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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73A ASP* 2.8 47.5 + - - +
76A LEU* 3.6 14.9 + - + +
77A PRO 2.8 29.6 + - - -
79A THR* 2.9 36.7 + - - +
161A CYS* 3.4 9.9 - - - -
162A SER* 1.3 78.9 - - - +
164A ALA* 1.3 65.2 + - - +
266A PRO* 4.3 3.4 - - - -
290A GLY 3.5 2.8 + - - -
291A LYS* 3.3 47.4 - - - +
292A ASP 3.5 10.8 - - - +
293A ARG* 3.5 3.8 - - - +
294A TRP* 2.9 42.5 + - + +
295A LEU* 4.3 0.2 - - - +
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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