Contacts of the strand formed by residues 98 - 106 (chain D) in PDB entry 4IHB
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 SER 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D VAL* 3.6 7.5 + - - -
94D THR* 3.3 18.9 - - - +
96D SER* 2.9 26.3 + - - -
97D LEU* 1.3 80.1 - - - +
99D ALA* 1.3 63.2 + - - +
120D GLN* 4.3 9.9 + - - -
121D VAL 3.2 13.0 - - - -
122D SER* 3.6 12.1 - - - -
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Residues in contact with ALA 99 (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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90D GLU* 4.1 22.9 - - + +
91D VAL* 4.2 4.0 - - + +
98D SER* 1.3 77.9 - - - +
100D SER* 1.3 62.7 + - - +
101D PHE* 3.8 25.8 - - + -
120D GLN* 3.5 5.0 - - - +
121D VAL* 2.8 32.9 + - - +
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Residues in contact with SER 100 (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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99D ALA* 1.3 75.7 - - - +
101D PHE* 1.3 72.6 + - - +
118D VAL* 6.1 2.0 - - - -
119D LEU 3.5 9.4 - - - -
120D GLN* 4.0 12.6 - - - +
212D FMT 4.5 15.9 - - - -
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Residues in contact with PHE 101 (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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86D VAL* 3.5 37.5 - - + -
87D PRO* 3.9 17.5 - - + -
90D GLU* 3.9 23.1 - - + -
91D VAL* 4.6 4.0 - - + -
99D ALA* 3.8 33.7 - - + -
100D SER* 1.3 78.3 - - - +
102D ASN* 1.3 58.9 + - - +
103D ALA* 3.6 11.0 - - + +
117D LEU 3.4 0.5 - - - +
118D VAL* 3.2 7.3 - - - +
119D LEU* 2.7 55.3 + - + +
121D VAL* 4.1 18.2 - - + -
212D FMT 5.0 2.9 - - - -
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Residues in contact with ASN 102 (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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8D TYR* 5.1 1.8 + - - -
10D GLU* 3.9 9.6 + - - +
101D PHE* 1.3 72.3 - - - +
103D ALA* 1.3 57.4 + - - +
104D PRO* 3.7 0.2 - - - +
116D SER* 3.6 12.0 + - - -
117D LEU 3.4 2.7 - - - +
118D VAL* 3.3 24.7 - - + +
212D FMT 3.2 31.3 + - - +
93E ALA 3.6 10.8 + - - +
94E THR* 3.9 2.9 + - - +
95E PRO* 3.1 48.8 - - + +
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Residues in contact with ALA 103 (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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84D ALA* 4.1 22.9 - - + -
86D VAL* 5.7 4.0 - - + -
101D PHE* 3.6 15.0 - - + -
102D ASN* 1.3 73.5 - - - +
104D PRO* 1.3 70.6 - - + +
105D LEU* 3.5 1.6 + - - +
116D SER* 3.1 2.4 - - - -
117D LEU* 2.8 43.6 + - + +
119D LEU* 4.8 5.2 - - + -
93E ALA 4.4 2.9 - - - +
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Residues in contact with PRO 104 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D GLU 4.1 3.1 - - - +
84D ALA* 4.1 8.0 - - - +
102D ASN 3.7 3.4 - - - +
103D ALA* 1.3 86.3 - - + +
105D LEU* 1.3 63.4 + - - +
106D LEU* 3.7 17.3 + - + +
112D PRO* 5.7 0.7 - - + -
113D THR 6.2 0.2 - - - +
115D ALA 3.4 9.4 - - - +
116D SER* 4.1 4.2 - - - -
92E LEU 3.4 27.8 - - - +
93E ALA 3.6 12.3 - - - +
94E THR 3.2 27.4 - - - +
95E PRO* 3.9 2.2 - - + -
97E LEU* 3.6 23.6 - - + -
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Residues in contact with LEU 105 (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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9D ALA* 4.9 4.0 - - + -
12D VAL* 5.4 2.0 - - + -
67D VAL 4.7 2.5 - - - +
69D VAL* 3.7 37.0 - - + -
81D LEU* 6.3 0.2 - - + -
82D GLY* 3.8 14.8 - - - +
83D GLU* 3.6 26.7 - - - +
84D ALA* 4.1 8.5 - - + +
103D ALA 4.3 0.9 - - - +
104D PRO* 1.3 72.3 - - - +
106D LEU* 1.3 62.3 + - - +
112D PRO* 4.0 0.2 - - - +
113D THR* 2.7 38.5 + - - +
115D ALA* 2.7 33.4 + - + +
116D SER* 4.1 17.9 - - - +
117D LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 106 (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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80D PHE* 3.5 3.5 - - - -
82D GLY* 3.4 4.0 - - - -
83D GLU* 2.8 40.0 + - + +
84D ALA* 5.6 2.5 - - - -
104D PRO* 4.0 16.6 - - + +
105D LEU* 1.3 80.8 - - - +
107D ASP* 1.3 64.9 + - - +
110D LYS* 3.8 34.5 - - + +
111D GLN 3.4 4.3 - - - +
112D PRO* 3.8 22.4 - - + -
113D THR* 3.7 2.7 - - - -
92E LEU* 3.9 33.9 - - + +
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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