Contacts of the strand formed by residues 104 - 108 (chain G) in PDB entry 1CA0
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 THR 104 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53G VAL* 3.7 4.2 - - - +
54G THR* 3.0 37.1 + - + +
55G ALA 3.9 7.2 - - - +
56G ALA* 3.0 25.7 + - - +
60G VAL* 5.2 4.0 - - + +
88G VAL* 3.4 33.7 - - + -
89G PHE 3.3 10.1 - - - +
90G LYS* 3.3 14.4 - - + +
103G ILE* 1.3 78.0 + - - +
105G LEU* 1.3 67.6 + - - +
106G LEU* 4.0 8.7 - - + -
237H TRP* 4.2 1.3 - - - -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ILE* 4.3 13.9 - - + -
51G TRP* 3.7 18.6 - - + -
52G VAL 3.6 11.2 - - - +
53G VAL* 4.3 13.0 - - + -
88G VAL* 3.4 3.5 - - - -
89G PHE* 2.7 49.7 + - + +
104G THR* 1.3 72.5 - - - +
106G LEU* 1.3 62.2 + - - +
237H TRP* 3.6 22.9 - - + -
238H VAL* 3.9 29.2 - - + +
241H THR* 3.5 35.7 - - + -
242H LEU* 4.0 7.0 - - + -
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Residues in contact with LEU 106 (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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33G LEU* 3.9 21.1 - - + -
50G ASN 3.6 0.3 - - - +
51G TRP* 3.4 8.9 - - - -
52G VAL* 2.9 51.2 + - + +
54G THR* 3.9 19.1 - - + -
60G VAL* 3.6 36.6 - - + -
66G VAL* 4.2 9.9 - - + -
85G ILE* 4.2 10.8 - - + -
87G LYS 3.6 2.7 - - - -
88G VAL* 3.8 22.4 - - + -
104G THR* 4.0 6.1 - - + -
105G LEU* 1.3 81.1 - - - +
107G LYS* 1.3 60.0 + - - +
108G LEU* 3.7 3.1 + - + +
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Residues in contact with LYS 107 (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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50G ASN* 3.4 31.3 - - - +
51G TRP* 3.4 34.4 - - + +
85G ILE* 3.6 1.7 - - - -
86G ALA* 2.6 38.7 + - + +
87G LYS* 2.9 20.3 + - + +
89G PHE* 4.1 8.1 - - + -
106G LEU* 1.3 71.5 - - - +
108G LEU* 1.3 62.7 + - - +
245H ASN* 2.6 32.0 + - + +
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Residues in contact with LEU 108 (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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46G LEU* 4.5 14.6 - - + -
49G GLU 3.7 18.6 - - - +
50G ASN* 2.8 28.2 + - - +
52G VAL* 4.3 9.6 - - + -
66G VAL* 3.8 32.5 - - + -
83G LEU* 3.7 29.2 - - + -
84G LYS 3.4 13.5 - - - +
85G ILE* 4.7 2.9 - - + -
86G ALA* 3.5 5.4 - - - +
106G LEU* 4.7 3.6 - - + +
107G LYS* 1.3 84.0 - - - +
109G SER* 1.3 62.3 + - - +
110G THR* 3.1 20.7 - - - +
111G ALA 5.1 0.2 + - - -
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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