Contacts of the strand formed by residues 104 - 108 (chain E) in PDB entry 1C9T
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 104 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E LEU* 4.6 0.2 - - + -
53E VAL* 3.5 6.6 - - - +
54E SER* 2.6 44.6 + - - +
55E ALA 3.6 16.4 - - - +
56E ALA* 3.5 12.3 - - + +
58E CYS* 4.1 5.6 - - + +
59E TYR* 3.3 48.5 - - - +
63E ILE* 4.6 2.5 - - + -
88E SER* 4.9 2.9 - - - -
89E ILE 3.4 18.4 - - - +
90E VAL* 3.6 11.7 - - + -
91E HIS 4.5 0.2 - - - +
103E ILE* 1.3 74.3 - - - +
105E LEU* 1.3 70.6 + - - +
106E ILE* 3.9 29.4 - - + -
237E TRP* 4.5 2.0 - - - -
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ILE* 4.4 3.8 - - + -
51E TRP* 3.7 19.8 - - + -
52E VAL 3.5 3.1 - - - +
53E VAL* 4.0 28.5 - - + -
87E LYS 4.0 0.7 - - - +
88E SER* 3.6 1.4 - - - -
89E ILE* 2.8 47.0 + - + +
104E MET* 1.3 73.6 - - - +
106E ILE* 1.3 61.6 + - - +
237E TRP* 3.7 23.8 - - + -
238E ILE* 3.8 35.7 - - + +
241E THR* 3.7 31.2 - - + -
242E ILE* 4.5 8.7 - - + -
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Residues in contact with ILE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.7 40.4 - - + -
50E GLN 3.9 0.2 - - - +
51E TRP* 3.3 8.3 - - - -
52E VAL* 2.7 55.4 + - + +
54E SER* 4.6 3.4 - - - -
63E ILE* 4.4 8.3 - - + -
65E VAL* 4.3 13.9 - - + -
85E ALA* 3.6 27.1 - - + -
87E LYS 3.6 3.1 - - - +
88E SER* 4.6 9.6 - - - +
104E MET* 3.9 22.9 - - + -
105E LEU* 1.3 77.6 - - - +
107E LYS* 1.3 66.1 + - - +
108E LEU* 4.0 2.0 + - + -
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Residues in contact with LYS 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLN* 3.4 37.5 + - - +
51E TRP* 3.7 29.6 - - + +
85E ALA* 3.3 4.3 - - - -
86E SER* 2.6 37.6 + - - -
87E LYS* 2.8 42.3 + - + +
106E ILE* 1.3 74.7 - - - +
108E LEU* 1.3 61.9 + - - +
245E ASN* 2.7 35.0 + - - +
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Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 4.5 0.9 - - + -
49E SER 3.5 22.9 - - - +
50E GLN* 2.8 36.2 + - - +
52E VAL* 4.1 20.4 - - + -
65E VAL* 3.5 38.1 - - + -
67E LEU* 4.4 6.5 - - + -
83E ILE* 3.7 18.4 - - + -
84E SER 3.6 3.8 - - - +
86E SER* 4.1 1.0 - - - -
106E ILE* 4.6 2.9 - - + -
107E LYS* 1.3 78.0 - - - +
109E LYS* 1.3 67.7 + - - +
110E SER 3.0 17.0 + - - +
112E ALA* 3.8 17.3 - - + -
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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