Contacts of the strand formed by residues 95 - 99 (chain D) in PDB entry 1H4O
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 ARG 95 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLU* 2.8 41.3 + - - +
23D VAL* 4.3 11.1 - - - +
28D LEU* 3.7 28.2 - - + +
69D VAL* 4.1 18.8 - - + +
70D VAL 2.8 17.1 + - - +
71D ALA* 3.2 10.0 - - + +
72D CYS 2.8 28.4 + - - +
92D GLY* 6.3 1.6 - - - +
93D LYS 6.1 0.4 - - - -
94D VAL* 1.3 73.7 - - - +
96D LEU* 1.3 62.2 + - - +
97D LEU* 3.7 9.2 + - + +
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Residues in contact with LEU 96 (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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16D GLU* 3.4 29.7 + - - +
17D GLY 4.5 1.2 + - - -
52D LEU* 4.5 6.7 - - + -
72D CYS* 3.7 17.5 - - + +
74D SER* 6.1 0.2 - - - +
81D THR* 3.7 25.7 + - + +
82D GLY* 5.1 2.9 - - - -
84D TRP* 3.7 34.1 - - + -
85D GLY* 3.6 30.1 - - - -
90D ALA* 3.7 10.8 - - + -
94D VAL* 3.4 22.2 + - + +
95D ARG* 1.3 73.5 - - - +
97D LEU* 1.3 59.8 + - - +
98D ALA 4.3 0.2 + - - -
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Residues in contact with LEU 97 (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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14D VAL* 4.0 8.5 - - + -
15D PHE 3.3 3.8 - - - +
16D GLU* 3.9 27.1 - - + +
23D VAL* 4.2 16.4 - - + -
25D LEU* 3.8 27.4 - - + -
28D LEU* 3.9 9.4 - - + -
36D LEU* 5.0 2.0 - - + -
71D ALA* 3.7 28.0 - - + -
72D CYS 2.8 17.8 + - - +
73D LEU* 3.4 14.0 - - + +
74D SER* 3.1 27.7 + - - -
81D THR* 4.2 4.4 - - - +
95D ARG* 4.2 7.2 - - + +
96D LEU* 1.3 82.0 - - - +
98D ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 98 (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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14D VAL* 3.4 5.5 - - - +
15D PHE* 2.7 40.5 + - + +
74D SER 3.7 4.3 - - - -
76D ASN 3.3 17.9 - - - +
77D ASP 3.7 0.7 - - - -
78D ALA* 3.6 21.8 - - + +
81D THR* 3.5 21.9 + - + +
97D LEU* 1.3 72.7 - - - +
99D ASP* 1.3 58.1 + - - +
100D PRO* 3.4 10.0 - - + +
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Residues in contact with ASP 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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13D GLU 4.8 2.9 - - - +
14D VAL* 4.0 13.9 - - + +
15D PHE* 5.3 0.6 - - - -
73D LEU* 3.9 17.8 - - + +
74D SER 2.9 15.4 + - - +
75D VAL* 3.3 17.1 - - + +
76D ASN 3.7 1.1 + - - -
97D LEU 4.2 0.2 + - - -
98D ALA* 1.3 72.6 - - - +
100D PRO* 1.3 65.8 - - - +
101D THR* 4.0 2.9 + - - -
102D GLY* 3.1 15.0 + - - -
103D ALA* 3.0 27.8 + - - +
104D PHE* 2.7 36.1 + - - +
105D GLY 4.2 0.9 + - - -
125D LEU* 5.5 1.2 - - - +
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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