Contacts of the strand formed by residues 95 - 101 (chain A) in PDB entry 3IMJ
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 PHE 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A PHE* 3.7 22.2 - + - -
85A ILE* 4.0 18.6 - - + -
86A ARG 3.2 15.3 - - - +
87A GLU* 3.7 22.2 - - + -
93A GLY 4.5 2.5 - - - -
94A ASP* 1.3 77.0 - - - +
96A SER* 1.3 66.4 + - - +
109A LYS* 3.7 6.2 - - - +
110A VAL* 3.1 42.5 + - + +
118A TYR* 4.0 20.4 - + - -
128A LEU* 4.0 12.6 - - + -
95B PHE* 3.5 35.2 - + - -
112B ARG* 5.5 1.3 - - - -
118B TYR* 3.4 25.8 - - - -
128B LEU* 4.1 4.5 - - + -
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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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1A AYI 3.1 28.3 + - - -
85A ILE* 3.5 5.4 - - - +
86A ARG* 2.8 65.3 + - - +
88A SER* 3.6 8.0 - - - -
95A PHE* 1.3 77.1 + - - +
97A LEU* 1.3 60.0 + - - +
108A PHE 3.4 12.1 - - - -
109A LYS* 4.2 2.3 - - - +
110A VAL* 4.1 4.9 - - - -
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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
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83A PHE* 3.6 26.0 - - + -
84A LEU 3.4 16.4 - - - +
85A ILE* 3.9 17.3 - - + -
96A SER* 1.3 73.2 - - - +
98A SER* 1.3 63.2 + - - +
99A VAL* 3.8 20.4 - - + -
106A GLN 3.6 1.2 - - - +
107A HIS* 3.4 3.6 - - - +
108A PHE* 2.8 56.7 + - + +
110A VAL* 4.2 6.7 - - + +
120A LEU* 4.1 14.4 - - + -
131A LEU* 5.1 5.8 - - + -
140A VAL* 3.9 27.6 - - + -
148A LEU* 4.3 8.7 - - + -
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Residues in contact with SER 98 (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 ALA* 3.9 10.2 - - - +
74A LEU* 3.3 19.1 - - - +
83A PHE* 3.2 5.5 - - - +
84A LEU* 3.1 35.8 + - - -
86A ARG* 2.8 24.0 + - - -
96A SER 4.2 0.4 - - - -
97A LEU* 1.3 70.3 - - - +
99A VAL* 1.3 60.7 + - - +
105A VAL* 4.3 0.7 - - - -
106A GLN 3.3 4.7 - - - -
107A HIS* 2.8 31.5 + - - -
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Residues in contact with VAL 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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74A LEU* 4.1 0.4 - - - +
81A GLY* 3.7 26.0 - - - +
82A ALA 3.5 2.7 - - - -
83A PHE* 4.3 0.2 - - + -
97A LEU* 3.8 12.6 - - + -
98A SER* 1.3 77.9 - - - +
100A LYS* 1.3 75.2 + - - +
101A PHE* 4.8 0.6 - - + +
105A VAL* 3.3 6.0 - - - +
106A GLN* 2.8 41.0 + - + +
108A PHE* 3.8 26.7 - - + -
140A VAL* 4.5 2.2 - - + -
146A ILE* 3.8 17.9 - - + -
148A LEU* 3.7 24.5 - - + -
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Residues in contact with LYS 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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74A LEU* 3.4 25.6 - - + +
75A SER* 3.3 19.8 + - - +
77A GLN* 3.2 30.3 + - + +
78A ARG 3.8 13.7 - - - -
79A HIS 3.4 20.0 - - - +
80A ASP* 4.0 10.3 - - - -
81A GLY* 2.8 27.8 + - - -
82A ALA* 2.8 19.3 + - + +
99A VAL* 1.3 75.3 - - - +
101A PHE* 1.3 62.9 + - - +
102A GLY* 3.3 21.1 + - - +
104A ASP 3.7 9.9 - - - +
105A VAL* 4.4 5.2 - - + +
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Residues in contact with PHE 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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80A ASP* 3.7 26.2 - - + -
99A VAL* 3.7 2.4 + - + +
100A LYS* 1.3 73.9 - - - +
102A GLY* 1.3 63.9 + - - +
103A ASN 3.5 0.5 + - - -
104A ASP* 2.9 28.4 + - - +
106A GLN* 4.0 17.8 + - - +
144A GLN* 3.5 38.8 - - + -
145A GLN 3.8 24.0 - - - -
146A ILE* 3.8 36.1 - - + -
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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