Contacts of the strand formed by residues 105 - 111 (chain A) in PDB entry 1CO1
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 SER 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ALA* 3.2 4.3 - - - -
68A GLY 2.7 36.3 + - - +
69A ASN* 4.9 5.8 + - - +
104A LYS* 1.3 72.1 - - - +
106A PHE* 1.3 59.0 + - - +
107A THR* 3.3 6.8 + - - -
125A ALA* 4.0 19.3 - - - -
126A ILE* 3.7 7.0 + - - -
127A LYS* 3.4 26.0 + - - +
128A ILE* 5.0 0.2 - - - -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 5.0 6.3 - - + -
36A PRO* 6.0 2.5 - - + -
37A THR* 3.4 30.3 - - + -
65A VAL* 4.2 7.9 - - + -
66A MET 5.2 1.6 - - - -
67A ALA* 4.1 11.9 - - + +
96A PHE* 3.4 32.5 - + + -
97A VAL* 6.0 1.1 - - + -
105A SER* 1.3 67.2 - - - +
107A THR* 1.3 58.0 + - - +
108A LEU* 3.0 48.3 + - + +
122A TYR* 4.2 22.0 - + - +
124A ARG 4.5 2.8 - - - +
125A ALA* 2.8 36.8 + - - +
126A ILE* 3.8 12.4 + - + +
128A ILE* 4.6 9.8 - - + +
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A MET* 2.8 42.0 + - + +
68A GLY* 4.6 7.0 + - - -
70A ASP* 5.4 5.9 + - - -
73A TYR* 5.8 11.5 - - + -
105A SER* 3.3 8.6 + - - -
106A PHE* 1.3 66.6 - - - +
108A LEU* 1.3 65.3 + - - +
109A THR* 3.3 8.6 + - + +
121A THR* 3.7 21.5 - - - +
122A TYR 6.1 0.9 - - - -
125A ALA* 4.6 8.8 - - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 5.7 0.9 - - + -
25A THR* 5.2 0.7 - - - -
32A CYS* 4.4 13.7 - - + -
34A VAL* 4.8 16.2 - - + -
63A VAL* 4.5 8.3 - - + -
64A THR 4.2 3.1 - - - -
65A VAL* 4.1 20.6 - - + +
96A PHE* 4.5 4.3 - - + -
106A PHE* 3.0 49.4 + - + -
107A THR* 1.3 68.5 - - - +
109A THR* 1.3 59.7 + - - +
110A ILE* 3.5 29.4 - - + -
121A THR* 3.7 2.8 + - - -
122A TYR* 3.0 55.9 + - + +
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.8 1.8 - - - +
64A THR* 2.8 67.0 + - + +
66A MET* 3.7 18.2 - - - -
107A THR* 3.3 8.3 + - + +
108A LEU* 1.3 76.1 - - - +
110A ILE* 1.3 66.3 + - - +
111A THR* 5.2 2.2 - - - +
119A VAL* 4.4 7.4 - - + +
120A ALA 2.5 26.1 + - - -
121A THR* 4.4 6.8 - - - -
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 3.7 33.2 - - + -
30A PHE* 5.1 12.1 - - + -
32A CYS* 4.0 13.2 - - - -
51A VAL* 5.9 1.3 - - + -
61A THR* 3.3 37.0 - - + +
62A LEU 3.7 4.5 - - - +
63A VAL* 3.9 18.4 - - + +
84A MET* 6.1 1.1 - - - -
108A LEU* 3.5 29.2 - - + -
109A THR* 1.3 71.5 - - - +
111A THR* 1.3 57.8 + - - +
112A VAL* 5.2 2.5 - - + -
118A GLN 3.3 8.6 - - - +
119A VAL* 3.4 1.0 - - - -
120A ALA* 2.8 41.5 + - + +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A THR* 3.6 1.6 - - - -
62A LEU* 2.7 62.0 + - + +
64A THR* 3.8 23.8 - - + -
109A THR* 3.7 4.3 + - - -
110A ILE* 1.3 70.4 - - - +
112A VAL* 1.3 65.9 + - - +
117A PRO* 5.3 2.6 - - - +
118A GLN 3.8 1.8 - - - -
119A VAL* 3.5 21.6 - - - +
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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