Contacts of the strand formed by residues 104 - 112 (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 ASP 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LYS* 3.7 0.9 - - - +
101A PHE 2.9 35.2 + - - +
102A GLY 3.3 2.5 - - - +
103A ASN* 1.3 93.2 + - - +
105A VAL* 1.3 70.3 + - - +
106A GLN* 3.9 16.5 + - + +
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Residues in contact with VAL 105 (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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71A GLU* 3.6 47.2 - - + +
74A LEU* 3.8 29.4 - - + -
75A SER* 3.9 20.0 - - - +
98A SER* 4.3 0.4 - - - -
99A VAL 3.3 13.0 - - - +
100A LYS* 4.4 4.7 - - + -
103A ASN 5.8 0.4 - - - +
104A ASP* 1.3 78.5 - - - +
106A GLN* 1.3 61.8 + - - +
107A HIS* 3.6 28.1 + - + -
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Residues in contact with GLN 106 (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 3.6 35.3 - - + +
97A LEU 3.6 1.0 - - - +
98A SER* 3.3 4.2 - - - -
99A VAL* 2.8 38.5 + - + +
101A PHE* 4.0 18.1 + - + +
104A ASP* 4.7 15.2 + - + +
105A VAL* 1.3 74.4 - - - +
107A HIS* 1.3 61.2 + - - +
108A PHE* 3.8 14.6 - - + -
141A SER* 4.7 0.9 + - - -
144A GLN* 3.0 26.5 + - - +
146A ILE* 3.3 25.4 - - - +
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Residues in contact with HIS 107 (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 2.8 48.5 + - + +
67A ARG* 3.4 54.3 - - + +
70A ALA* 4.7 0.2 - - + -
71A GLU* 2.9 40.8 + - + +
86A ARG* 3.1 14.2 + - - +
97A LEU 3.4 2.5 - - - -
98A SER* 2.8 34.8 + - - -
105A VAL* 3.6 16.3 + - + -
106A GLN* 1.3 72.6 - - - +
108A PHE* 1.3 56.7 + - - +
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Residues in contact with PHE 108 (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 3.3 46.0 - - + +
96A SER* 3.4 7.1 - - - -
97A LEU* 2.8 56.2 + - + +
99A VAL* 3.8 25.6 - - + -
106A GLN* 3.8 35.0 - - + -
107A HIS* 1.3 74.4 - - - +
109A LYS* 1.3 61.0 + - - +
120A LEU* 4.1 16.4 - - + -
121A TRP* 4.0 8.1 - + - -
140A VAL* 3.2 42.6 - - + -
141A SER* 4.3 3.4 - - - -
146A ILE* 4.8 1.1 - - + -
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Residues in contact with LYS 109 (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 2.7 83.1 + - + +
88A SER* 4.5 3.1 - - - -
90A SER* 4.8 2.7 + - - -
91A ALA* 3.9 26.4 - - - +
94A ASP* 4.6 11.8 + - + +
95A PHE 3.7 17.7 - - - +
96A SER* 4.2 3.1 - - - +
108A PHE* 1.3 72.6 - - - +
110A VAL* 1.3 67.2 + - - +
111A LEU* 3.4 25.1 + - + +
120A LEU* 3.6 4.8 - - - +
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Residues in contact with VAL 110 (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 ILE* 4.3 15.3 - - + -
94A ASP* 4.7 6.8 - - - +
95A PHE* 3.1 43.7 + - + +
96A SER* 4.1 12.6 - - - +
97A LEU* 4.2 3.4 - - + +
109A LYS* 1.3 77.3 - - - +
111A LEU* 1.3 64.2 + - - +
112A ARG* 5.3 1.2 - - - +
118A TYR* 3.8 33.6 - - + -
119A PHE 3.8 2.9 - - - -
120A LEU* 4.1 12.3 - - + -
128A LEU* 3.9 11.7 - - + -
131A LEU* 4.1 13.0 - - + -
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Residues in contact with LEU 111 (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 4.0 11.7 - - - +
109A LYS* 3.8 26.7 - - + +
110A VAL* 1.3 74.5 - - - +
112A ARG* 1.3 62.5 + - - +
118A TYR* 3.3 8.4 - - - +
119A PHE* 2.9 68.4 + - + +
120A LEU 3.7 21.3 - - - +
121A TRP 5.4 0.2 - - - +
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Residues in contact with ARG 112 (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 ASP* 5.7 4.9 - - - +
110A VAL 4.2 0.6 + - - +
111A LEU* 1.3 76.9 - - - +
113A ASP* 1.3 64.3 + - - +
116A GLY* 3.2 38.3 + - - +
117A LYS 3.3 9.0 - - - +
118A TYR* 4.0 20.1 - - + -
119A PHE* 3.9 4.1 - - - -
92B PRO 4.2 1.8 + - - -
93B GLY* 2.9 32.5 + - - -
94B ASP* 3.0 19.4 + - - -
112B ARG* 3.8 27.9 - - - +
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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