Contacts of the strand formed by residues 80 - 87 (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 PHE 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D VAL* 3.6 16.6 - - + -
70D LYS* 4.0 16.1 - - + +
78D ASN* 2.9 17.8 - - + +
79D ARG* 1.3 78.4 - - - +
81D LEU* 1.3 64.8 + - - +
82D GLY* 3.9 6.1 - - - -
83D GLU* 3.1 56.3 - - + -
106D LEU 3.5 10.8 - - - -
107D ASP* 3.6 11.0 - - - -
108D THR* 3.6 41.7 - - + -
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Residues in contact with LEU 81 (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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12D VAL* 3.8 31.9 - - + -
13D HIS 4.4 7.0 - - - +
14D THR* 3.7 31.9 - - + -
15D PRO* 5.7 0.4 - - + -
22D ALA* 5.1 2.5 - - + -
69D VAL* 2.9 22.0 + - + +
70D LYS 4.2 4.3 - - - +
71D ASP* 3.6 37.7 - - + +
73D GLU* 5.4 2.5 - - - +
78D ASN 5.8 0.4 - - - +
79D ARG* 3.3 3.1 + - - +
80D PHE* 1.3 85.4 - - - +
82D GLY* 1.3 58.7 + - - +
105D LEU* 6.3 0.2 - - + -
107D ASP* 4.9 1.6 - - - +
113D THR* 3.8 17.0 - - - +
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Residues in contact with GLY 82 (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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68D VAL* 3.5 2.8 - - - +
69D VAL* 2.7 31.0 + - - +
80D PHE* 3.8 5.7 - - - -
81D LEU* 1.3 82.1 - - - +
83D GLU* 1.3 60.1 + - - +
105D LEU* 3.8 24.2 - - - -
106D LEU 3.4 11.7 - - - -
113D THR* 4.5 1.3 - - - -
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Residues in contact with GLU 83 (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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66D HIS* 2.6 38.0 + - + +
67D VAL 3.2 12.6 - - - +
68D VAL* 3.9 3.7 - - + +
80D PHE* 3.1 33.6 - - + -
82D GLY* 1.3 76.1 - - - +
84D ALA* 1.3 65.2 + - - +
85D LYS* 5.7 3.2 - - + +
105D LEU* 3.6 6.1 - - - +
106D LEU* 2.8 42.2 + - + +
107D ASP 4.4 1.0 - - - +
108D THR* 5.6 0.5 - - - -
110D LYS* 3.4 30.6 + - - -
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Residues in contact with ALA 84 (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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65D LEU 3.6 1.6 - - - +
66D HIS* 3.4 3.2 - - - -
67D VAL* 2.8 39.1 + - + +
83D GLU* 1.3 76.3 - - - +
85D LYS* 1.3 65.5 + - - +
86D VAL* 3.8 6.9 - - + +
103D ALA* 4.1 26.0 - - + -
104D PRO 4.1 9.0 - - - +
105D LEU* 4.1 8.9 - - + +
106D LEU* 5.6 3.1 - - - -
117D LEU* 5.8 2.7 - - + -
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Residues in contact with LYS 85 (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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64D GLU* 3.7 33.2 + - + +
65D LEU 3.6 4.9 - - - +
66D HIS* 3.7 24.9 - - + +
83D GLU* 5.7 3.4 - - + +
84D ALA* 1.3 76.0 - - - +
86D VAL* 1.3 63.5 + - - +
87D PRO* 3.5 8.1 - - - +
110D LYS* 5.1 15.9 - - - +
61E GLN* 4.5 19.9 - - - +
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Residues in contact with VAL 86 (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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64D GLU* 3.5 2.5 - - - -
65D LEU* 3.0 47.6 + - + +
67D VAL* 4.7 4.7 - - + -
84D ALA* 4.4 12.6 - - + +
85D LYS* 1.3 71.5 - - - +
87D PRO* 1.3 64.5 - - + +
88D LEU* 3.3 15.9 + - + -
101D PHE* 3.5 44.6 - - + -
103D ALA* 5.7 3.4 - - + -
119D LEU* 4.1 24.7 - - + -
121D VAL* 4.8 0.9 - - + -
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Residues in contact with PRO 87 (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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61D GLN 6.0 0.2 - - - +
63D SER 4.2 4.9 - - - +
64D GLU* 4.3 14.6 - - + +
85D LYS 3.5 9.2 - - - +
86D VAL* 1.3 82.8 - - + +
88D LEU* 1.3 59.0 + - - +
89D ARG* 2.9 36.2 + - + +
90D GLU* 3.2 36.5 + - + +
101D PHE* 3.9 13.0 - - + -
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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