Contacts of the strand formed by residues 169 - 175 (chain I) in PDB entry 3CII
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 LYS 169 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D ARG* 5.4 11.2 - - - +
72D GLN* 5.2 0.9 + - - -
79I GLN* 4.4 25.1 + - + +
80I LYS* 3.4 12.1 - - - +
81I THR* 5.4 6.1 - - - +
84I GLU* 6.0 1.1 - - - -
167I GLU 5.4 1.6 - - - +
168I ASP* 1.3 86.8 + - - +
170I ASN* 1.3 75.3 + - - +
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Residues in contact with ASN 170 (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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72D GLN* 3.3 19.8 + - - +
78I GLU 4.0 0.7 - - - +
79I GLN* 3.4 14.4 + - - +
80I LYS* 2.7 41.0 + - - +
114I PHE* 3.9 16.3 - - - +
116I TRP* 3.3 39.3 - - + +
154I ALA* 5.0 4.3 - - - -
164I GLU* 3.3 31.1 + - - +
168I ASP* 4.8 1.2 + - - +
169I LYS* 1.3 83.1 + - - +
171I ARG* 1.3 67.4 + - - +
172I TYR* 4.0 1.7 + - - -
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Residues in contact with ARG 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ARG* 3.2 39.8 - - - +
76I SER* 3.4 33.9 + - - +
77I SER* 3.8 7.0 + - - +
78I GLU 3.7 10.3 - - - +
79I GLN* 3.8 14.5 + - - +
113I GLN* 2.8 50.8 + - + +
114I PHE 3.6 6.9 + - - +
115I TYR* 3.3 26.7 + - + -
116I TRP* 2.5 31.1 + - - +
170I ASN* 1.3 81.0 + - - +
172I TYR* 1.3 52.3 + - - +
164J LYS* 4.4 8.9 - - - +
168J ILE* 4.1 22.2 - - - +
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Residues in contact with TYR 172 (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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74I PHE* 3.8 23.3 - + - -
76I SER* 3.2 41.3 + - - -
78I GLU* 3.5 17.3 + - - -
80I LYS* 4.0 26.9 - - + -
85I SER* 3.8 26.5 - - - -
88I LEU* 4.5 16.2 + - + +
89I CYS* 4.3 4.9 - - - -
92I GLN* 5.3 0.9 + - - -
96I LEU* 4.1 2.7 - - + -
115I TYR* 3.4 5.6 - - - -
116I TRP* 3.5 26.5 - - + +
170I ASN 4.5 3.8 - - - -
171I ARG* 1.3 75.7 - - - +
173I ILE* 1.3 81.7 + - - +
174I CYS* 3.6 24.5 - - - -
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Residues in contact with ILE 173 (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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73I TYR* 4.6 12.6 - - + -
74I PHE 3.1 12.8 - - - +
75I ILE* 4.4 9.4 - - + +
96I LEU* 3.4 9.4 - - - +
97I LEU* 3.1 60.8 + - + +
105I LEU* 4.3 4.0 - - + -
108I MET* 3.9 26.5 - - + -
115I TYR* 4.0 27.6 - - + -
116I TRP 3.5 5.1 + - - +
117I ILE* 5.2 0.2 - - + -
155I TYR* 6.0 0.7 - - + -
157I PRO* 5.6 0.2 - - + -
172I TYR* 1.3 84.3 - - - +
174I CYS* 1.3 78.9 + - - +
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Residues in contact with CYS 174 (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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65I TRP* 3.8 13.9 - - + -
73I TYR* 3.5 4.0 - - - -
74I PHE* 2.9 38.8 + - + -
88I LEU 4.8 1.3 - - - -
89I CYS* 2.0 47.8 - - - -
92I GLN* 5.4 1.1 - - - -
94I SER* 3.0 16.6 - - - +
95I SER 3.4 3.8 - - - -
172I TYR* 3.6 19.3 - - - -
173I ILE* 1.3 83.9 - - - +
175I LYS* 1.3 63.6 + - - +
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Residues in contact with LYS 175 (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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71I ASN* 3.6 21.1 - - - +
72I CYS 3.4 5.4 - - - +
73I TYR* 3.7 22.7 - - + -
94I SER* 3.5 6.1 - - - -
95I SER* 3.0 39.2 + - - +
97I LEU* 3.8 16.6 - - + -
98I GLN* 3.6 35.9 + - - +
100I GLN* 5.5 5.0 - - - +
104I GLU* 3.5 21.4 + - - -
174I CYS* 1.3 78.6 - - - +
176I GLN* 1.3 68.7 + - - +
177I GLN* 3.7 24.7 + - - +
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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