Contacts of the strand formed by residues 67 - 73 (chain C) in PDB entry 3K75
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 PHE 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C SER* 3.3 1.8 - - - -
66C ALA* 1.3 91.3 - - + +
68C VAL* 1.3 70.8 + - - +
69C GLU 4.3 0.4 - - - -
90C THR* 3.8 23.1 - - + -
91C SER 3.1 10.5 - - - +
92C SER* 3.4 28.5 - - - +
94C MET 5.7 1.1 - - - -
96C PRO* 6.3 0.2 - - + -
131C VAL 4.4 0.4 - - - -
132C CYS* 3.2 1.6 - - - -
133C SER* 2.7 50.5 + - - +
135C PRO* 4.8 4.7 - - + -
136C TYR* 3.5 35.7 - + - -
291E PHE* 3.7 25.6 - + - -
300E PRO* 4.2 10.5 - - + -
311E LEU* 3.9 16.8 - - + -
322E TYR* 4.4 6.1 - + - -
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.9 27.4 - - + -
62C ASN* 4.7 0.7 - - - +
65C SER* 4.3 7.9 - - - -
67C PHE* 1.3 81.8 - - - +
69C GLU* 1.3 61.4 + - - +
70C VAL* 4.0 3.8 + - + +
88C LEU* 4.9 4.2 - - - +
89C VAL 3.9 2.6 - - - +
90C THR* 4.4 0.4 - - - -
91C SER* 2.7 31.3 + - - +
93C PHE* 3.4 34.0 - - + -
130C ILE* 4.2 13.0 - - + -
131C VAL 3.3 3.6 - - - +
132C CYS* 3.8 26.0 - - - -
144C LEU* 4.1 8.7 - - + -
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE 4.3 0.4 - - - -
68C VAL* 1.3 73.4 - - - +
70C VAL* 1.3 69.3 + - - +
71C LEU* 4.8 3.4 - - + -
86C VAL* 3.7 24.8 - - - +
88C LEU 3.7 13.0 - - - +
89C VAL* 5.4 0.2 - - - -
90C THR* 3.2 30.4 + - + +
129C LYS 3.7 1.4 - - - +
130C ILE* 3.6 0.3 - - - -
131C VAL* 2.7 52.8 + - + +
302E GLY* 3.0 14.6 - - - -
303E VAL* 2.7 38.8 + - - +
304E THR* 4.2 2.6 + - - -
306E VAL* 4.9 2.9 - - - +
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 4.7 5.6 - - + -
60C ILE* 3.7 30.3 - - + -
68C VAL* 4.0 6.7 + - + -
69C GLU* 1.3 76.9 - - - +
71C LEU* 1.3 69.5 + - - +
86C VAL* 4.2 2.8 - - - +
87C LEU* 3.5 16.2 + - + -
88C LEU* 3.1 48.2 + - + +
128C VAL* 5.0 2.0 - - + -
129C LYS 3.6 3.6 - - - +
130C ILE* 4.6 13.2 - - + +
147C VAL* 5.6 1.6 - - + -
149C PHE* 3.7 31.9 - - + -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLU* 4.5 8.5 - - + +
70C VAL* 1.3 76.4 - - - +
72C VAL* 1.3 57.8 + - - +
81C GLU* 5.8 0.9 - - + +
84C TYR* 3.6 21.1 - - + +
85C GLU 3.1 40.4 - - - +
86C VAL* 3.2 15.0 - - + +
87C LEU 4.5 0.9 - - - +
128C VAL* 3.2 5.5 - - - +
129C LYS* 2.5 63.1 + - + +
131C VAL* 5.2 1.1 - - + -
303E VAL* 3.2 35.0 - - + -
304E THR* 3.8 13.0 - - + -
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ILE* 4.9 6.5 - - + -
71C LEU* 1.3 75.3 - - - +
73C GLY* 1.3 68.0 + - - +
84C TYR* 3.2 8.5 - - - -
85C GLU 2.7 56.1 + - - +
86C VAL 4.8 0.2 - - - -
87C LEU* 4.0 23.3 - - + +
120C ALA* 5.1 2.2 - - + +
125C TRP* 3.2 51.9 - - + +
127C ARG 3.1 17.0 - - - +
128C VAL* 4.2 11.7 - - + -
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Residues in contact with GLY 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C VAL* 1.3 79.5 - - - +
74C SER* 1.3 60.3 + - - -
83C ASP 3.9 8.5 - - - -
84C TYR* 3.5 14.8 - - - -
125C TRP* 3.4 17.6 - - - +
126C ASP 3.4 4.9 + - - -
127C ARG* 2.9 34.0 + - - +
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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