Contacts of the strand formed by residues 88 - 96 (chain D) in PDB entry 1S9C
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 LEU 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B LEU 6.0 1.8 - - - +
86D LYS* 4.7 10.3 - - - +
87D VAL* 1.3 83.2 - - - +
89D HIS* 1.3 62.3 + - - +
90D GLY* 3.7 0.8 + - - -
144D LEU* 3.4 5.7 - - - -
145D PHE* 2.8 59.1 + - + +
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Residues in contact with HIS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D MET* 4.4 13.1 - - + +
87D VAL 4.3 0.2 + - - -
88D LEU* 1.3 74.7 - - - +
90D GLY* 1.3 59.4 + - - +
91D GLU 3.0 23.7 + - - -
92D GLN* 2.9 28.3 + - - -
142D PHE* 3.6 21.0 - + - +
143D SER 3.7 8.1 - - - -
144D LEU* 4.5 11.7 - - + -
217D LEU* 4.1 27.1 - - + +
246D PHE* 3.6 26.0 - + + +
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LEU* 3.7 3.0 + - - -
89D HIS* 1.3 74.1 - - - +
91D GLU* 1.3 67.5 + - - +
143D SER* 2.9 17.1 + - - -
145D PHE* 5.1 7.0 - - - +
245D ARG* 3.5 3.8 - - - +
246D PHE* 2.8 33.1 + - - +
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D HIS* 3.0 21.3 + - - -
90D GLY* 1.3 82.6 - - - +
92D GLN* 1.3 61.4 + - - +
141D GLN 4.6 0.2 - - - -
143D SER* 3.2 35.4 + - - +
161D VAL* 4.8 9.9 - - - +
162D LYS 4.5 1.7 - - - +
163D VAL* 5.4 0.2 - - - -
164D ALA* 3.7 5.2 + - - +
243D LYS* 3.1 30.2 + - - +
244D ALA 3.2 8.5 - - - +
245D ARG* 2.6 49.6 + - + +
246D PHE* 4.2 2.9 - - - -
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Residues in contact with GLN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 4.2 7.7 - - + +
89D HIS* 2.9 26.5 + - - -
91D GLU* 1.3 75.2 - - - +
93D TYR* 1.3 75.2 + - - +
140D ASN* 3.3 30.7 + - - +
141D GLN 3.8 6.5 - - - +
142D PHE* 3.2 18.8 - - - -
217D LEU* 3.9 16.8 - - + -
220D PHE* 4.0 22.1 - - + -
242D VAL 4.0 0.8 - - - +
243D LYS* 3.2 8.8 - - - +
244D ALA 2.9 31.1 + - - +
246D PHE* 4.0 19.3 - - + -
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Residues in contact with TYR 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLN* 1.3 83.9 + - - +
94D LEU* 1.3 61.8 + - - +
95D GLU* 2.9 45.7 + - + +
139D HIS* 4.0 11.9 - + - -
140D ASN* 3.3 4.7 - - - -
141D GLN* 2.8 45.1 + - + +
162D LYS* 3.5 60.0 + - + -
241D ALA* 3.9 13.2 - - + +
242D VAL 3.3 15.7 - - - -
243D LYS* 3.9 16.2 - - + +
285D TYR* 3.9 17.3 - + - -
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PRO 3.5 24.9 - - - +
59D THR* 3.8 17.9 - - + -
61D GLY* 4.1 3.8 - - - -
62D VAL* 3.9 21.3 - - + +
92D GLN* 4.9 0.2 - - - +
93D TYR* 1.3 79.0 - - - +
95D GLU* 1.3 68.9 + - - +
96D LEU* 4.1 11.9 - - + -
138D CYS* 4.1 12.3 - - + -
139D HIS 3.3 16.4 - - - +
140D ASN* 3.4 25.1 - - - +
220D PHE* 5.3 0.4 - - + -
239D PHE* 5.8 2.5 - - + -
241D ALA* 3.0 6.1 - - - +
242D VAL* 2.9 43.7 + - + +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D TYR* 2.9 32.0 + - + +
94D LEU* 1.3 75.7 - - - +
96D LEU* 1.3 67.6 + - - +
97D TYR* 3.3 44.6 + - + -
138D CYS* 3.3 5.5 - - - +
139D HIS* 2.9 35.5 + - + +
162D LYS* 4.5 7.4 + - - -
240D LYS* 3.4 12.6 - - + +
241D ALA* 3.9 4.5 - - + -
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PRO* 3.4 42.8 - - + +
94D LEU* 4.1 14.1 - - + -
95D GLU* 1.3 77.5 - - - +
97D TYR* 1.3 64.6 + - - +
98D LYS* 3.0 13.1 + - - +
99D PRO* 5.2 2.2 - - + -
100D LEU* 4.0 24.9 - - + +
137D ILE 3.8 2.0 - - - -
138D CYS* 3.8 23.1 - - + -
236D VAL* 5.5 2.0 - - + +
239D PHE* 3.4 27.9 - - + +
240D LYS* 2.7 24.7 + - - +
241D ALA* 5.8 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