Contacts of the strand formed by residues 44 - 50 (chain I) 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 GLN 44 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G GLY* 3.8 5.7 - - - -
44G GLN* 4.9 5.7 - - - +
46G LEU* 5.3 3.5 - - - +
92G MET* 3.6 35.8 - - - +
94G THR* 2.6 42.2 + - - +
44H GLN* 5.1 4.2 - - - +
42I VAL* 3.4 13.6 - - - +
43I VAL* 1.3 84.3 - - + +
45I MET* 1.3 63.8 + - - +
46I LEU* 4.9 9.7 - - + +
72I PRO* 3.3 18.8 - - + +
92I MET 4.6 0.2 - - - -
93I MET* 3.7 0.3 - - - -
94I THR* 2.9 41.6 + - + +
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Residues in contact with MET 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G MET* 4.9 0.9 - - - +
28I LEU* 3.7 27.4 - - + -
42I VAL* 4.3 0.9 - - + -
44I GLN* 1.3 75.4 - - - +
46I LEU* 1.3 72.4 + - - +
47I LEU* 4.5 4.9 - - + -
62I VAL* 4.0 18.8 - - + -
68I TRP* 3.4 35.9 - - + -
71I VAL* 4.2 10.3 - - + -
72I PRO 2.9 4.1 + - - +
73I VAL* 3.3 18.5 - - + -
74I THR* 3.2 22.1 + - - +
91I VAL* 3.7 18.4 - - + -
92I MET 3.4 6.7 - - - +
93I MET* 3.8 20.0 - - + -
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Residues in contact with LEU 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU* 3.6 18.6 - - + -
92G MET* 4.8 5.6 - - + -
44H GLN* 5.4 2.5 - - - +
46H LEU* 3.6 41.3 - - + -
44I GLN* 4.9 8.1 - - + +
45I MET* 1.3 79.1 - - - +
47I LEU* 1.3 65.0 + - - +
74I THR* 3.2 31.9 - - + +
76I MET* 3.8 25.8 - - + -
91I VAL* 3.3 6.1 - - - +
92I MET* 3.0 45.7 + - + +
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I THR* 3.8 29.4 - - + -
28I LEU* 5.0 2.0 - - + -
45I MET* 4.5 7.2 - - + -
46I LEU* 1.3 80.2 - - - +
48I SER* 1.3 59.8 + - - +
58I PRO* 4.0 26.0 - - + +
59I ALA* 3.8 28.0 - - + -
62I VAL* 4.4 11.7 - - + -
73I VAL* 4.1 17.5 - - + -
74I THR 3.1 7.3 + - - +
75I CYS* 3.0 13.8 - - - +
76I MET* 2.9 27.5 + - - +
89I ILE* 4.7 3.4 - - + -
90I ARG 3.3 7.0 - - - +
91I VAL* 4.6 15.5 - - + -
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Residues in contact with SER 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H THR* 5.0 1.4 + - - +
75H CYS 4.6 2.2 + - - -
47I LEU* 1.3 76.0 - - - +
49I ALA* 1.3 59.8 + - - +
58I PRO* 5.1 1.1 - - - -
76I MET* 3.1 33.9 - - - +
78I GLU* 4.0 17.5 - - - +
88I CYS 3.9 0.5 - - - +
89I ILE* 3.2 8.6 - - - +
90I ARG* 2.9 54.6 + - - +
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Residues in contact with ALA 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G MET* 3.5 34.8 - - + +
48I SER* 1.3 74.2 - - - +
50I THR* 1.3 64.7 + - - +
53I LEU* 4.0 23.1 - - + -
58I PRO* 4.2 9.0 - - + -
76I MET 3.2 6.7 + - - -
77I GLN* 3.7 7.1 - - - +
78I GLU* 3.1 21.8 + - - -
88I CYS 3.5 4.9 - - - -
89I ILE* 4.5 1.3 - - + +
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Residues in contact with THR 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H PHE* 5.9 2.5 - - + -
49I ALA* 1.3 76.3 - - - +
51I PRO* 1.3 60.5 - - + +
52I ASP* 2.6 39.8 + - - +
53I LEU* 2.8 17.2 + - - +
78I GLU* 4.2 14.8 - - + -
79I MET 5.3 2.0 - - - +
80I ASP* 6.4 0.2 - - - -
85I LEU 3.5 22.0 - - - +
86I LYS* 4.9 7.2 - - - +
87I LYS* 3.3 2.6 + - - -
88I CYS 2.9 31.3 + - - +
90I ARG* 4.0 13.7 - - - +
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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