Contacts of the strand formed by residues 2 - 11 (chain D) in PDB entry 2CHT
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 MET 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D ILE* 1.3 86.9 + - - +
4D ARG* 3.5 41.3 - - - +
96D GLN* 3.4 11.3 - - - +
97D THR 2.8 42.6 + - - +
98D ASP* 4.3 9.3 - - - +
3F ILE* 4.3 7.9 - - + -
40F GLU 4.4 0.9 - - - +
41F ASP 3.3 22.7 - - - +
43F VAL* 3.5 13.5 - - + -
96F GLN* 3.2 51.4 - - - +
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Residues in contact with ILE 3 (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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2D MET* 1.3 102.9 - - - +
4D ARG* 1.3 61.8 + - - +
43D VAL* 3.9 18.4 - - + -
94D THR* 3.7 12.6 - - + -
95D VAL 2.9 10.1 - - - +
96D GLN* 4.0 13.0 - - + -
2E MET* 4.9 2.9 - - - -
3E ILE* 3.3 37.7 - - + +
3F ILE* 3.8 20.2 - - + +
43F VAL* 3.3 36.0 - - + +
94F THR* 4.5 2.9 - - + -
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Residues in contact with ARG 4 (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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2D MET* 3.5 31.1 - - + +
3D ILE* 1.3 81.8 - - - +
5D GLY* 1.3 66.4 + - - +
94D THR* 3.4 0.8 - - - -
95D VAL* 2.7 38.6 + - - +
97D THR* 3.8 19.2 + - + +
98D ASP* 5.5 1.8 - - - +
99D VAL 3.7 21.4 + - - -
100D PRO* 4.3 3.0 - - - +
101D GLN* 3.7 37.5 + - - +
104D ILE* 4.1 13.9 - - + -
40F GLU* 2.9 34.2 + - - +
42F VAL 3.9 11.3 + - - -
43F VAL* 3.7 9.9 - - - +
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Residues in contact with GLY 5 (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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4D ARG* 1.3 77.6 - - - +
6D ILE* 1.3 59.6 + - - -
7D ARG 4.0 0.2 - - - -
92D MET* 3.3 9.9 - - - -
93D MET 3.1 8.5 - - - -
104D ILE* 3.7 15.2 - - - +
106D HIS* 4.0 1.4 + - - -
43F VAL 2.8 18.4 + - - -
44F GLN* 3.3 19.2 - - - +
72F PRO* 3.7 12.0 - - - +
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Residues in contact with ILE 6 (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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5D GLY* 1.3 74.9 - - - -
7D ARG* 1.3 64.1 + - - +
8D GLY 4.0 0.5 + - - -
31D ILE* 3.8 19.2 - - + +
35D ASN* 3.5 22.7 - - + +
37D THR* 3.8 20.6 - - - +
91D VAL* 3.9 2.9 - - - +
92D MET* 3.3 1.8 - - - +
93D MET* 2.7 41.1 + - + +
95D VAL* 3.7 35.4 - - + -
104D ILE* 3.7 17.5 - - + -
105D ARG 3.5 25.1 - - - +
106D HIS* 4.0 4.3 - - + -
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Residues in contact with ARG 7 (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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6D ILE* 1.3 73.6 - - - +
8D GLY* 1.3 84.2 + - - +
31D ILE* 4.6 2.4 - - - +
90D ARG* 3.5 16.5 - - - +
91D VAL 3.1 15.1 + - - +
92D MET* 3.5 26.5 - - + +
106D HIS* 3.2 26.9 - - + +
107D VAL 3.1 20.1 + - - -
108D TYR* 3.3 20.5 + - - +
206D TSA 2.7 48.3 + - - +
72F PRO* 3.6 17.7 - - + -
73F VAL 3.0 21.2 + - - +
74F THR* 3.5 15.4 + - - -
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Residues in contact with GLY 8 (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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7D ARG* 1.3 87.2 + - - +
9D ALA* 1.4 58.4 - - - -
27D LEU* 4.1 1.3 - - - -
31D ILE* 3.8 8.7 - - - -
90D ARG* 3.3 0.3 - - - -
91D VAL* 2.8 47.7 + - - +
107D VAL 3.3 12.1 - - - -
108D TYR* 4.8 2.2 - - - -
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Residues in contact with ALA 9 (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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7D ARG* 4.7 0.2 - - - +
8D GLY* 1.4 74.4 - - - +
10D THR* 1.3 53.9 + - - +
27D LEU* 3.7 6.7 - - - +
88D CYS* 4.5 3.8 - - - -
89D ILE 3.3 11.2 - - - +
90D ARG* 3.9 15.0 - - + +
107D VAL 3.0 8.8 + - - +
108D TYR* 3.4 28.0 - - + -
109D LEU 2.8 31.7 + - - -
112D ALA* 3.5 11.4 - - + +
115D LEU* 5.1 0.4 - - + -
206D TSA 4.4 3.8 - - - +
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Residues in contact with THR 10 (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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9D ALA* 1.3 72.1 - - - +
11D THR* 1.3 72.0 + - - +
23D LYS* 3.7 35.4 + - + +
27D LEU* 3.8 17.7 - - + +
88D CYS* 3.3 11.4 - - - -
89D ILE* 2.9 45.8 + - + -
109D LEU* 3.7 16.8 - - - +
110D GLU* 3.1 23.4 - - - +
112D ALA* 4.1 1.8 - - - -
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Residues in contact with THR 11 (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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10D THR* 1.3 88.4 + - - +
12D VAL* 1.3 68.8 + - - +
13D GLU* 6.1 0.2 - - - -
23D LYS* 3.9 9.5 - - - +
85D LEU* 3.8 31.4 - - + -
86D LYS 3.8 15.9 - - - +
87D LYS 3.1 8.1 - - - +
88D CYS* 4.2 1.8 - - - -
89D ILE 4.8 0.4 - - - +
110D GLU* 3.3 10.3 - - - +
111D LYS* 2.9 36.3 + - + +
112D ALA 3.9 7.4 - - - +
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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
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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