Contacts of the strand formed by residues 88 - 96 (chain A) in PDB entry 1SCR
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 TRP 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO* 3.5 17.0 - - + +
87A GLU* 1.3 101.9 + - + +
89A VAL* 1.3 64.3 + - - +
178A PRO* 3.7 30.3 - - + -
179A VAL 3.4 18.4 - - - -
180A HIS* 3.6 52.2 + + + -
217A ILE* 3.8 21.5 + - + +
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Residues in contact with VAL 89 (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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85A LEU* 4.1 10.8 - - + -
86A PRO* 3.6 22.0 - - + +
88A TRP* 1.3 78.8 - - - +
90A ARG* 1.3 61.0 + - - +
91A VAL* 4.7 2.0 - - + -
178A PRO* 3.4 5.7 - - - +
179A VAL* 2.7 43.6 + - + +
181A ILE* 3.9 28.5 - - + -
214A ILE* 3.5 27.6 - - + -
215A SER 3.2 15.7 - - - +
217A ILE* 3.8 6.5 - - - -
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Residues in contact with ARG 90 (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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89A VAL* 1.3 77.5 - - - +
91A VAL* 1.3 61.6 + - - +
141A ILE* 3.5 28.0 - - - +
174A LEU* 3.9 22.2 - - + -
175A PHE 3.6 14.3 + - - +
176A TYR* 2.8 36.2 + - - -
177A ALA 4.4 1.2 - - - +
178A PRO* 4.3 16.5 - - + +
179A VAL* 4.9 2.9 - - - +
213A PHE* 5.2 0.2 - - - -
214A ILE* 3.5 3.8 - - - +
215A SER* 3.0 33.8 + - - +
217A ILE* 2.7 55.2 + - + +
218A ASP* 4.9 1.0 - - - +
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Residues in contact with VAL 91 (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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89A VAL* 4.7 3.6 - - + -
90A ARG* 1.3 76.7 - - - +
92A GLY* 1.3 58.4 + - - +
109A TRP* 3.8 3.3 - - + -
111A PHE* 3.8 36.1 - - + -
128A PHE* 4.1 31.0 - - + -
174A LEU* 3.3 7.0 - - - +
175A PHE* 3.2 29.0 + - + +
179A VAL* 4.4 13.6 - - + +
181A ILE* 6.4 0.2 - - + -
212A PHE* 4.2 9.4 - - + -
213A PHE* 3.4 6.5 - - - +
214A ILE* 4.1 24.2 - - + -
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Residues in contact with GLY 92 (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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91A VAL* 1.3 75.9 - - - +
93A LEU* 1.3 62.2 + - - -
109A TRP* 3.6 9.1 - - - -
173A ALA 3.1 14.6 - - - -
174A LEU* 4.0 2.0 - - - -
212A PHE* 3.4 11.1 - - - -
213A PHE* 2.9 45.2 + - - -
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Residues in contact with LEU 93 (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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92A GLY* 1.3 80.8 - - - +
94A SER* 1.3 61.3 + - - +
106A ILE* 3.9 31.6 - - + -
109A TRP* 3.7 37.0 - - + +
154A LEU* 4.6 4.5 - - + -
156A LEU* 4.0 18.7 - - + +
172A ARG* 3.2 6.4 - - - +
173A ALA* 3.0 30.9 + - + +
195A PHE* 3.9 35.4 - - + -
210A ILE* 5.0 2.5 - - + -
211A ALA 3.3 5.4 - - - +
212A PHE* 3.9 17.9 - - + -
213A PHE* 3.7 1.0 - - - -
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Residues in contact with SER 94 (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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93A LEU* 1.3 77.2 - - - +
95A ALA* 1.3 63.2 + - - +
156A LEU* 4.0 2.5 - - - -
171A GLY 3.6 6.6 + - - -
172A ARG* 3.3 24.8 - - - +
210A ILE* 3.4 4.0 - - - +
211A ALA* 2.8 33.1 + - - +
213A PHE* 3.9 3.8 - - - -
230A LEU 2.8 25.9 + - - -
231A GLY* 3.8 2.3 - - - -
232A LEU* 3.7 21.9 - - - +
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Residues in contact with ALA 95 (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 SER* 1.3 79.5 + - - +
96A SER* 1.3 64.5 + - - +
104A ASN* 3.5 31.0 - - + +
156A LEU* 3.7 16.2 - - + -
157A THR* 3.4 4.0 - - + +
170A VAL* 3.5 3.6 - - - +
171A GLY 3.2 27.4 + - - +
209A GLY 3.3 16.8 - - - +
210A ILE* 4.1 1.8 - - + -
230A LEU* 4.4 5.2 - - - -
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Residues in contact with SER 96 (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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95A ALA* 1.3 77.9 - - - +
97A THR* 1.3 68.4 + - - +
104A ASN* 3.5 6.7 - - - +
157A THR* 3.7 2.7 - - - -
169A SER 3.2 14.4 - - - -
170A VAL* 4.1 9.4 - - - -
208A ASP* 2.9 25.3 + - - +
209A GLY 3.5 4.6 + - - -
226A THR 4.2 0.9 - - - -
227A GLY 2.7 35.3 + - - -
230A LEU* 3.2 19.0 - - - +
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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