Contacts of the strand formed by residues 44 - 50 (chain K) in PDB entry 2CHS
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 GLN 44 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44J GLN* 4.8 8.3 - - - +
42K VAL* 3.3 9.4 - - - +
43K VAL* 1.3 87.2 - - + +
45K MET* 1.3 62.8 - - - +
46K LEU* 4.8 11.2 - - + +
72K PRO* 3.4 16.8 - - + +
92K MET 5.9 0.2 - - - +
94K THR* 2.8 40.5 + - - +
5L GLY* 3.7 15.0 - - - -
44L GLN* 4.8 5.4 - - - +
46L LEU* 5.3 4.3 - - - +
92L MET* 3.8 27.9 - - - +
94L THR* 2.7 39.2 + - - +
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Residues in contact with MET 45 (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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28K LEU* 3.7 32.3 - - + -
42K VAL* 4.9 0.4 - - + -
44K GLN* 1.3 77.4 - - - +
46K LEU* 1.3 73.3 + - - +
47K LEU* 4.4 10.1 - - + -
62K VAL* 4.3 7.9 - - + -
68K TRP* 3.6 35.2 - - + -
71K VAL* 3.9 6.3 - - + -
72K PRO 3.0 9.3 + - - +
73K VAL* 3.2 43.8 - - + -
74K THR 3.3 4.2 + - - -
91K VAL* 3.5 20.4 - - + -
92K MET 3.4 5.8 - - - +
93K MET* 4.1 12.8 - - + -
92L MET* 4.7 1.0 - - - +
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Residues in contact with LEU 46 (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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44J GLN* 5.2 3.1 - - - +
46J LEU* 3.8 37.0 - - + -
44K GLN* 4.8 14.1 - - + +
45K MET* 1.3 80.8 - - - +
47K LEU* 1.3 62.0 + - - +
74K THR* 3.2 31.9 - - + +
76K MET* 4.0 22.4 - - + -
91K VAL* 3.4 6.9 - - - +
92K MET* 3.0 44.6 + - + +
46L LEU* 3.9 19.1 - - + -
76L MET* 4.9 2.2 - - + -
92L MET* 4.8 4.7 - - + -
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Residues in contact with LEU 47 (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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24K THR* 3.6 27.8 - - + -
27K LEU* 6.0 0.9 - - + -
28K LEU* 4.9 5.4 - - + -
45K MET* 4.4 15.9 - - + -
46K LEU* 1.3 77.5 - - - +
48K SER* 1.3 60.9 + - - +
58K PRO* 4.3 8.7 - - + +
59K ALA* 3.6 35.2 - - + +
62K VAL* 4.5 11.7 - - + -
73K VAL* 4.6 6.5 - - + -
74K THR 3.0 6.4 + - - +
75K CYS* 3.1 17.2 - - - +
76K MET* 3.0 24.6 + - - +
89K ILE* 4.3 11.9 - - + -
90K ARG 3.3 5.2 - - - +
91K VAL* 4.1 19.3 - - + -
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Residues in contact with SER 48 (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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74J THR* 4.8 1.6 + - - -
75J CYS 4.7 0.6 + - - -
47K LEU* 1.3 76.5 - - - +
49K ALA* 1.3 61.7 + - - +
58K PRO* 5.5 1.6 - - - -
76K MET* 3.2 36.5 - - - +
78K GLU* 4.1 22.7 + - - +
88K CYS 3.9 0.2 - - - +
89K ILE* 3.3 8.5 - - - +
90K ARG* 3.0 49.7 + - - +
79L MET* 5.4 1.3 - - - -
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Residues in contact with ALA 49 (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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48K SER* 1.3 76.7 - - - +
50K THR* 1.3 67.8 + - - +
51K PRO 3.7 0.7 - - - -
53K LEU* 3.8 23.3 - - + -
58K PRO* 4.6 3.4 - - + -
76K MET 3.3 6.3 + - - -
77K GLN* 3.7 8.0 - - - +
78K GLU* 2.9 22.0 + - - -
88K CYS 3.4 4.9 - - - +
89K ILE* 4.5 4.9 - - + -
79L MET* 3.9 30.4 - - + +
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Residues in contact with THR 50 (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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57J PHE* 6.1 1.1 - - + -
49K ALA* 1.3 79.0 - - - +
51K PRO* 1.3 67.4 - - + +
52K ASP* 2.7 34.2 + - - +
53K LEU* 3.3 13.7 + - - +
78K GLU* 4.0 9.4 - - + +
79K MET 5.3 1.8 - - - +
85K LEU 3.3 24.9 - - - +
86K LYS* 5.0 0.9 - - - -
87K LYS* 3.2 2.3 + - - -
88K CYS* 2.9 37.5 + - + +
90K ARG* 4.0 14.4 - - - +
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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