Contacts of the strand formed by residues 130 - 135 (chain G) in PDB entry 1KD1
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 GLU 130 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G MET 3.5 8.5 - - - +
85G GLU* 4.3 13.8 - - + +
125G GLU 4.3 0.3 - - - +
126G ILE* 3.7 3.7 - - - +
127G ASP* 2.9 38.2 + - + +
128G GLY 3.2 1.2 - - - -
129G GLU* 1.3 84.7 - - - +
131G LEU* 1.3 64.3 + - - +
170G ARG* 5.3 7.4 + - - -
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Residues in contact with LEU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLY* 3.4 4.2 - - - -
84G MET* 2.7 54.7 + - + +
86G VAL* 5.5 5.6 - - + +
95G VAL* 4.2 22.4 - - + -
97G VAL* 5.3 1.1 - - + -
102G VAL* 6.1 0.2 - - + -
124G VAL* 3.7 26.5 - - + -
125G GLU 3.7 3.1 - - - +
126G ILE* 3.3 38.4 - - + -
130G GLU* 1.3 77.5 - - - +
132G THR* 1.3 61.2 + - - +
133G VAL 4.2 0.4 - - - -
148G ILE* 4.5 6.3 - - + -
166G VAL* 3.7 29.8 - - + -
170G ARG* 5.4 0.2 + - - -
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Residues in contact with THR 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G GLU* 3.9 25.8 + - - +
82G TYR 3.3 8.4 + - - -
123G ASP 3.2 5.2 - - - +
124G VAL* 3.6 0.6 - - - -
125G GLU* 3.0 52.7 + - + +
131G LEU* 1.3 77.0 - - - +
133G VAL* 1.3 62.8 + - - +
134G SER* 3.8 3.0 + - - +
170G ARG* 4.7 9.9 + - - -
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G GLU* 3.0 4.3 - - - +
82G TYR* 2.7 46.5 + - + +
84G MET* 3.2 36.1 - - + -
122G THR* 3.4 28.7 - - + -
123G ASP 3.5 4.0 - - - +
124G VAL* 4.3 7.0 - - + -
132G THR* 1.3 74.1 - - - +
134G SER* 1.3 61.4 + - - +
141G VAL* 3.8 23.2 - - + +
144G THR* 4.0 10.5 - - + -
145G ALA* 4.1 8.7 - - + +
148G ILE* 4.5 5.4 - - + -
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Residues in contact with SER 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G TRP 2.8 14.4 - - - -
81G GLU* 3.3 26.0 + - - -
122G THR* 3.4 3.8 - - - -
123G ASP* 2.8 54.5 + - - +
125G GLU* 5.6 2.6 - - - +
132G THR* 4.5 4.0 + - - +
133G VAL* 1.3 77.8 - - - +
135G GLY* 1.3 60.3 + - - +
141G VAL* 3.9 7.9 - - - -
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Residues in contact with GLY 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ASN* 4.3 6.3 - - - -
79G GLY 3.8 0.3 - - - -
80G TRP* 2.9 37.2 + - - +
121G ASP 4.1 6.1 - - - -
123G ASP* 4.6 3.8 - - - -
134G SER* 1.3 76.1 - - - +
136G PRO* 1.3 70.1 - - - +
137G ASP 3.5 2.2 - - - -
141G VAL* 3.6 11.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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