Contacts of the strand formed by residues 96 - 104 (chain K) in PDB entry 5D4D
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 THR 96 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94K LEU* 4.0 9.9 - - - +
95K GLN* 1.3 80.5 - - + +
97K VAL* 1.3 70.9 + - - +
98K THR* 4.8 2.6 + - - -
143K ARG* 3.6 30.6 + - - +
144K VAL 3.4 6.4 + - - -
145K ASP* 3.3 21.3 - - - +
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Residues in contact with VAL 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K PHE* 3.5 28.0 - - + -
94K LEU* 3.5 26.5 - - + -
96K THR* 1.3 82.0 + - - +
98K THR* 1.3 69.6 + - - +
99K LEU* 3.5 23.3 + - + +
117K VAL* 4.5 16.2 - - + -
120K VAL* 3.7 17.7 - - + -
142K VAL 3.6 0.9 - - - +
143K ARG* 4.7 0.2 - - - -
144K VAL* 2.9 35.4 + - + +
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Residues in contact with THR 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K THR* 4.9 3.6 + - - -
97K VAL* 1.3 77.5 - - - +
99K LEU* 1.3 65.3 + - - +
100K LEU* 3.7 16.5 + - + +
117K VAL* 4.6 7.1 - - - +
141K GLU* 4.1 28.5 - - + +
142K VAL 3.4 12.1 - - - +
143K ARG* 4.5 4.3 - - - +
160K ASP* 4.2 17.2 + - - +
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Residues in contact with LEU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K LEU* 4.6 6.3 - - + -
87K VAL* 4.4 10.8 - - + -
97K VAL* 3.5 33.9 - - + +
98K THR* 1.3 72.6 - - - +
100K LEU* 1.3 62.4 + - - +
114K PHE* 3.4 39.2 - - + -
115K LEU 5.3 2.0 - - - +
117K VAL* 5.0 9.6 - - + -
120K VAL* 4.6 9.9 - - + -
122K ILE* 3.7 31.0 - - + -
140K MET 3.9 0.3 - - - +
141K GLU* 3.5 4.7 - - - -
142K VAL* 2.9 35.9 + - + +
144K VAL* 4.2 15.3 - - + -
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Residues in contact with LEU 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K THR* 3.7 17.7 + - + +
99K LEU* 1.3 77.2 - - - +
101K LEU* 1.3 60.8 + - - +
102K LYS* 5.7 9.9 - - - +
114K PHE* 3.3 5.5 - - - -
115K LEU* 2.8 61.0 + - + +
117K VAL* 5.5 1.7 - - + +
139K ASN* 6.2 0.2 - - - +
140K MET 3.6 2.9 - - - +
141K GLU* 3.8 29.8 - - + +
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Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K LEU* 1.3 76.0 - - - +
102K LYS* 1.3 68.1 + - - +
103K ALA* 3.8 18.6 - - + +
109K VAL* 3.7 31.4 - - + -
110K LYS 4.3 1.6 - - - +
113K ASP* 3.8 19.3 - - + +
114K PHE* 3.7 43.1 - - + +
115K LEU* 5.3 1.1 - - - -
129K ILE* 4.2 4.0 - - + -
138K LEU* 3.8 5.8 - - + +
139K ASN* 3.2 6.5 + - - +
140K MET* 2.9 60.8 + - + +
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Residues in contact with LYS 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K LEU* 5.7 11.5 - - - +
101K LEU* 1.3 75.1 - - - +
103K ALA* 1.3 61.7 + - - +
107K LYS* 5.6 0.5 + - - -
113K ASP 4.9 4.3 + - - +
115K LEU* 5.6 12.4 - - + +
138K LEU 3.5 2.0 - - - +
139K ASN* 3.4 42.0 - - + +
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Residues in contact with ALA 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K LEU* 3.8 13.7 - - + +
102K LYS* 1.3 76.4 - - - +
104K GLU* 1.3 67.0 + - - +
107K LYS* 3.8 27.8 - - + +
109K VAL* 3.8 19.7 - - + -
113K ASP* 5.4 0.9 - - + -
132K LEU* 4.1 2.2 - - + -
137K ARG* 3.7 1.2 - - - +
138K LEU* 2.9 33.2 + - + +
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Residues in contact with GLU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ALA* 1.3 79.5 - - - +
105K GLY* 1.3 70.9 + - - +
107K LYS* 3.3 17.2 - - - +
132K LEU* 3.8 3.6 - - - -
136K GLY 3.4 7.0 - - - -
137K ARG* 3.2 42.6 + - + +
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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