Contacts of the strand formed by residues 103 - 107 (chain D) in PDB entry 1XDM
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 VAL 103 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.1 9.6 - - + -
21D SER* 4.1 23.8 - - - +
22D ILE* 4.3 6.3 - - + -
74D GLY 3.2 20.1 + - - +
75D GLY* 2.9 5.1 - - - -
76D VAL 2.7 32.2 + - - -
101D GLY 4.7 5.6 - - - +
102D ILE* 1.3 74.0 - - - +
104D VAL* 1.3 56.2 + - - +
143D ASP* 3.2 42.4 - - + +
144D PHE* 4.3 7.2 - - + -
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Residues in contact with VAL 104 (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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76D VAL 3.4 5.2 - - - +
78D LEU* 3.6 29.2 - - + -
83D LEU* 4.7 11.9 - - + -
94D ARG* 3.7 15.5 - - + +
97D LEU* 3.7 34.1 - - + -
98D LYS* 4.7 4.3 - - + +
102D ILE 4.0 2.2 - - - +
103D VAL* 1.3 79.4 - - - +
105D GLY* 1.3 66.1 + - - +
141D GLY 4.0 15.3 - - - +
142D VAL* 3.3 4.9 - - + +
143D ASP* 3.0 28.9 + - - -
144D PHE* 3.4 7.5 - - - -
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Residues in contact with GLY 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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76D VAL 2.4 22.1 + - - +
77D ILE* 3.5 6.7 - - - -
78D LEU* 2.8 22.5 + - - +
104D VAL* 1.3 76.4 - - - +
106D ILE* 1.3 61.5 + - - +
142D VAL* 3.8 2.9 - - - -
144D PHE* 3.0 32.6 - - - -
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Residues in contact with ILE 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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77D ILE* 3.5 7.5 - - - +
78D LEU* 2.9 33.4 - - + +
79D PHE 3.7 17.3 - - - +
80D HIS 3.9 2.5 - - - +
83D LEU* 4.1 15.7 - - + -
105D GLY* 1.3 76.4 - - - +
107D LYS* 1.3 63.2 + - - +
108D LEU* 2.9 28.6 + - + +
137D TYR* 3.1 48.0 - - + +
142D VAL* 3.8 16.8 - - + -
144D PHE 3.0 13.2 + - - +
145D GLY* 4.8 1.3 - - - -
146D LYS 3.4 13.5 + - - -
182D LEU* 5.3 2.2 - - + -
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Residues in contact with LYS 107 (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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33D ASP* 3.4 39.1 + - + +
34D GLU* 5.1 0.8 - - - +
35D SER* 4.5 13.9 + - - +
77D ILE* 3.8 3.0 - - - +
78D LEU 3.0 18.4 + - - +
79D PHE* 3.7 32.6 - - + -
80D HIS* 5.0 2.6 + - - +
106D ILE* 1.3 73.3 - - - +
108D LEU* 1.3 59.0 + - - +
109D ASP* 3.2 31.8 + - + +
133D ARG* 4.5 6.1 + - - -
137D TYR* 4.9 0.9 + - - -
146D LYS* 4.2 16.2 - - + +
148D ARG* 3.6 26.0 - - - +
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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