Contacts of the strand formed by residues 71 - 78 (chain A) in PDB entry 2UYK
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 ILE 71 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.9 28.3 - - + -
61A VAL* 4.2 19.1 - - + -
67A SER 4.4 0.7 - - - +
68A VAL* 3.0 35.4 + - + +
69A GLY 4.4 1.2 - - - +
70A ASP* 1.3 78.8 - - - +
72A ILE* 1.3 64.6 + - - +
73A LYS 3.8 9.4 - - - +
74A MET* 3.8 29.6 - - + -
94A PHE* 5.1 2.9 - - + -
95A PHE* 4.4 10.5 - - + -
101A THR 4.7 4.3 - - - +
103A PRO* 3.6 17.2 - - + +
123A ALA* 4.2 3.4 - - + -
124A ILE 3.5 11.7 - - - +
125A ALA* 3.9 5.4 - - + -
2B LYS* 4.3 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP 3.7 2.0 - - - +
71A ILE* 1.3 77.3 - - - +
73A LYS* 1.3 70.3 + - + +
103A PRO* 3.4 8.5 - - - +
104A THR* 2.9 28.6 + - - +
124A ILE* 2.8 25.5 + - + +
125A ALA* 4.5 0.2 - - - -
126A VAL* 3.6 39.5 - - + -
2B LYS* 3.7 20.0 - - + +
21B VAL* 4.0 19.6 - - + +
23B LEU* 4.1 12.8 - - + -
28B PHE* 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.8 1.0 - - - +
72A ILE* 1.3 92.3 - - + +
74A MET* 1.3 73.4 + - - +
75A THR* 3.9 13.2 - - - +
103A PRO* 3.7 0.8 - - - +
104A THR* 3.3 20.4 - - - +
105A ARG* 5.3 1.1 - - - +
106A SER* 6.0 0.7 - - - +
122A GLU* 3.9 2.4 - - - +
123A ALA* 3.3 4.2 - - - -
124A ILE* 2.9 45.6 + - + +
28B PHE* 3.4 34.7 - - + -
29B THR 5.0 7.0 + - - +
122B GLU* 3.0 39.3 + - - +
123B ALA 5.3 1.2 + - - -
124B ILE* 4.3 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.5 6.3 - - + -
57A VAL* 4.3 5.2 - - + -
71A ILE* 3.8 14.4 - - + -
73A LYS* 1.3 79.5 - - - +
75A THR* 1.3 63.3 + - - +
76A VAL* 4.1 9.4 - - + -
91A TYR* 3.1 37.7 - - - +
94A PHE* 6.2 0.2 - - + -
95A PHE* 3.7 18.2 - - - -
103A PRO* 3.6 12.8 - - + -
104A THR 3.0 5.6 + - - +
105A ARG* 3.1 24.1 - - - +
106A SER 3.2 3.3 + - - -
121A ILE* 3.8 19.3 - - + -
122A GLU 3.3 5.8 - - - +
123A ALA* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 3.9 17.9 - - - +
74A MET* 1.3 75.2 + - - +
76A VAL* 1.3 63.7 + - - +
77A PHE* 3.6 34.4 - - + -
106A SER* 3.6 17.3 - - - +
108A VAL* 5.9 1.1 - - + -
120A GLU 3.6 2.1 - - - +
121A ILE* 3.3 5.0 - - - +
122A GLU* 2.9 55.5 + - - +
77B PHE* 4.9 7.6 - - + -
122B GLU* 4.3 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A MET* 4.4 2.2 - - + -
75A THR* 1.3 76.0 - - - +
77A PHE* 1.3 61.4 + - - +
78A ILE* 3.5 22.9 - - + -
84A PHE* 5.9 0.7 - - + -
87A ILE* 4.8 9.6 - - + -
91A TYR* 4.0 17.3 - - + -
105A ARG* 4.0 26.0 - - + -
106A SER 2.9 11.2 + - - +
107A CYS* 3.3 16.1 - - + -
108A VAL* 3.2 23.4 + - - +
119A LEU* 4.5 8.3 - - + -
120A GLU 3.7 2.9 - - - -
121A ILE* 4.2 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.6 32.3 - - + -
76A VAL* 1.3 71.5 - - - +
78A ILE* 1.3 62.4 + - - +
108A VAL* 3.6 25.8 - - + -
110A VAL* 3.9 13.2 - - + -
113A LEU* 3.7 11.2 - - + +
119A LEU* 3.1 3.8 - - - +
120A GLU* 2.9 49.2 + - + +
122A GLU* 4.4 9.9 - - + -
77B PHE* 4.4 14.4 - + - -
75C THR* 4.9 7.6 - - + -
77C PHE* 4.5 12.6 - + - -
106C SER* 4.4 16.6 - - - -
108C VAL* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.5 26.5 - - + +
77A PHE* 1.3 79.8 - - - +
79A THR* 1.3 63.2 + - - +
80A ASP 3.7 24.0 - - - +
81A LEU* 3.7 28.3 - - + -
83A ASP* 6.1 0.2 - - - +
84A PHE* 4.5 9.0 - - + -
87A ILE* 4.0 17.5 - - + -
107A CYS* 4.0 11.2 - - - -
108A VAL 3.0 17.2 + - - +
109A GLN* 3.1 10.9 - - - -
110A VAL* 2.8 27.2 + - - +
113A LEU* 4.6 0.2 - - - -
118A LYS 3.2 8.7 - - - +
119A LEU* 3.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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