Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 4L1O
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 GLU 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 5.0 2.9 - - - +
95A ASP* 1.3 74.6 - - - +
97A LEU* 1.3 61.6 + - - +
98A TYR* 3.8 24.0 - - + -
427A CYS 3.6 1.0 - - - +
428A LEU* 3.5 5.5 - - - +
429A VAL* 2.8 58.7 + - + +
370B ASP* 5.6 3.3 - - - +
374B LYS* 5.2 7.3 + - - -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 3.4 5.4 - - - +
86A VAL* 3.1 35.1 + - + +
87A GLU 4.0 8.5 - - - +
88A LYS* 4.5 12.2 - - + +
89A THR* 5.4 1.1 - - + +
92A THR* 4.0 23.1 - - - +
95A ASP* 3.6 24.7 + - + +
96A GLU* 1.3 79.2 - - - +
98A TYR* 1.3 64.5 + - - +
427A CYS 3.5 3.4 - - - -
428A LEU* 3.7 14.4 - - + -
396B LEU* 3.8 21.5 - - + -
398B SER* 3.4 24.5 - - - +
399B LEU* 4.5 8.3 - - + -
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Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.3 40.3 + - + -
84A GLU 3.1 21.8 - - - +
85A PRO* 3.9 3.8 - - + -
86A VAL* 4.3 4.6 - - - +
96A GLU* 3.8 28.9 - - + -
97A LEU* 1.3 79.5 - - - +
99A ILE* 1.3 68.8 + - - +
100A HIS* 4.1 5.4 - - + -
426A SER* 3.9 1.0 - - - -
427A CYS* 3.0 56.0 + - + +
429A VAL* 4.1 20.5 - - + +
374B LYS* 4.3 15.3 - - - +
377B ILE* 3.6 24.8 - - + +
399B LEU* 4.2 2.2 - - - +
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Residues in contact with ILE 99 (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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82A ALA 4.4 1.2 - - - +
83A ASP* 3.5 3.3 - - - -
84A GLU* 2.8 42.3 + - + +
86A VAL* 3.8 19.1 - - + -
98A TYR* 1.3 77.6 - - - +
100A HIS* 1.3 63.1 + - - +
101A SER* 4.0 3.3 + - - +
424A ARG* 3.8 56.5 - - + +
425A ARG 3.6 6.1 - - - +
426A SER* 3.7 25.4 - - - +
399B LEU* 4.2 7.9 - - + -
400B PRO* 4.0 20.2 - - + -
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Residues in contact with HIS 100 (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 ARG* 4.7 4.1 + - - -
83A ASP* 2.9 28.4 + - - +
98A TYR* 3.9 4.5 + - + -
99A ILE* 1.3 73.0 - - - +
101A SER* 1.3 73.5 + - - +
102A GLU* 3.3 29.0 + - - +
423A HIS 3.4 2.4 - - - +
424A ARG 3.8 0.2 - - - -
425A ARG* 2.8 43.5 + - + +
427A CYS* 3.7 22.0 - - - -
377B ILE* 3.8 33.0 + - + +
378B ALA* 4.5 13.1 - - + -
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Residues in contact with SER 101 (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 ARG* 5.2 1.0 + - - -
80A TRP 4.1 5.8 + - - -
81A ALA 4.5 17.1 + - - +
82A ALA 5.2 2.6 + - - -
83A ASP* 4.6 2.0 + - - -
99A ILE* 4.0 4.3 + - - +
100A HIS* 1.3 84.5 + - - +
102A GLU* 1.3 62.1 + - - +
418A PHE* 3.9 33.7 - - - -
422A SER* 4.6 4.9 - - - -
423A HIS 3.6 6.1 - - - -
424A ARG* 4.3 22.7 + - - +
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Residues in contact with GLU 102 (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 ARG* 3.9 12.5 + - - +
100A HIS* 3.3 11.6 + - + -
101A SER* 1.3 76.3 - - - +
103A PRO* 1.3 77.8 - - + +
130A ALA 4.6 0.4 - - - -
422A SER* 3.3 6.3 - - - -
423A HIS* 2.7 55.4 + - + +
425A ARG* 2.9 39.7 + - - -
380B THR 3.5 4.9 - - - +
381B SER* 2.5 34.9 + - - +
382B SER 3.7 0.2 + - - -
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Residues in contact with PRO 103 (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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14A PHE* 3.6 15.4 - - + -
20A ARG* 3.5 37.9 - - - +
25A ARG* 4.5 7.4 - - - +
102A GLU* 1.3 99.0 - - + +
104A LEU* 1.3 64.5 + - - +
130A ALA 3.3 23.5 - - - +
131A GLY* 3.4 26.7 - - - +
132A ASN* 3.5 7.2 - - - +
421A PHE 4.3 3.4 - - - +
423A HIS* 4.8 0.9 - - - +
359B LYS* 4.8 4.2 + - - -
381B SER* 4.9 3.3 + - - -
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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