Contacts of the strand formed by residues 113 - 121 (chain B) in PDB entry 1P27
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 LEU 113 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.8 6.5 - - + -
81B HIS 3.4 17.5 - - - +
82B GLU* 3.1 31.8 + - - +
84B ALA* 3.1 35.7 - - + +
104B LEU* 3.3 44.4 - - + +
105B ASN 3.6 4.7 - - - +
106B LEU* 3.7 21.8 - - + +
107B ASP* 4.1 3.2 - - - +
111B GLY 5.6 0.2 - - - +
112B TYR* 1.3 75.7 - - - +
114B LYS* 1.3 70.5 + - - +
115B GLY* 3.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.7 4.7 - - - +
63A ILE* 4.1 33.2 + - + +
66A ASP* 5.5 8.1 - - - +
128A ASP* 3.0 31.7 + - + +
80B VAL* 4.5 0.3 - - - +
105B ASN* 3.0 19.0 + - + +
106B LEU 4.5 1.8 - - - +
107B ASP* 2.9 42.6 + - + +
112B TYR 3.5 2.8 + - - -
113B LEU* 1.3 87.6 - - - +
115B GLY* 1.3 64.4 + - - +
116B TYR* 3.1 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 4.3 3.4 - - - -
62A ARG* 3.4 24.8 - - - +
78B THR* 3.7 1.3 - - - -
79B GLY* 3.2 13.0 + - - -
80B VAL* 2.9 43.5 + - - +
114B LYS* 1.3 73.1 - - - +
116B TYR* 1.3 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.3 29.6 - - + +
63A ILE* 4.1 14.1 - - + -
128A ASP 4.4 1.8 + - - -
131A CYS* 4.0 2.4 - - - +
132A LEU* 3.3 36.3 + - + +
76B PHE* 3.9 28.7 - + + -
77B VAL 3.1 12.1 - - - +
78B THR* 4.5 1.1 - - - +
80B VAL* 4.7 0.8 - - - +
103B HIS 5.8 0.7 - - - -
104B LEU* 4.4 3.3 - - - +
105B ASN* 2.9 54.4 + - + +
114B LYS* 3.1 34.6 + - + +
115B GLY* 1.3 74.3 - - - +
117B THR* 1.3 70.0 + - - +
118B LEU* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU 3.7 0.2 - - - +
76B PHE* 3.8 2.1 - - - -
77B VAL* 2.9 46.7 + - - +
80B VAL* 3.6 14.1 - - - +
89B ILE* 4.1 18.9 - - + +
102B ILE* 3.9 16.6 - - + -
103B HIS 3.0 22.7 - - - +
104B LEU* 3.5 17.6 - - + +
116B TYR* 1.3 80.0 + - - +
118B LEU* 1.3 73.7 + - - +
119B VAL* 4.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 5.1 1.1 - - + -
135A SER* 4.2 17.9 - - - +
136A LEU* 4.0 25.4 - - + +
139A LEU* 3.9 32.3 - - + +
74B ILE* 4.1 17.3 - - + -
75B LEU 3.3 7.0 - - - +
76B PHE* 3.8 24.7 - - + -
101B ASN 4.2 0.6 - - - +
102B ILE* 3.5 5.9 - - - -
103B HIS* 3.2 34.1 + - + +
116B TYR* 4.0 16.6 - - + -
117B THR* 1.3 80.1 - - - +
119B VAL* 1.3 62.6 + - - +
149B CYS* 4.2 4.0 - - - -
150B PHE* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 6.5 0.2 - - - -
73B TRP 3.8 1.4 - - - +
74B ILE* 3.4 3.2 - - - -
75B LEU* 2.8 41.0 + - + +
77B VAL* 4.3 10.5 - - + -
89B ILE* 3.8 28.0 - - + -
93B PHE* 4.1 27.4 - - + -
99B ILE* 4.0 20.2 - - + -
101B ASN 3.8 2.7 - - - -
102B ILE* 4.4 3.8 - - + -
117B THR* 4.3 4.9 - - + -
118B LEU* 1.3 79.4 - - - +
120B GLU* 1.3 61.5 + - - +
121B TYR* 4.0 26.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 3.9 17.0 - - + +
142A LYS* 3.1 11.7 + - - -
69B SER* 4.1 2.1 - - - -
71B GLU 3.8 10.0 + - - -
72B GLY* 3.7 29.4 + - - +
73B TRP 3.5 4.3 - - - +
74B ILE* 3.8 25.3 - - + +
99B ILE* 3.5 9.2 - - - +
100B LYS* 3.0 30.9 + - + +
101B ASN* 2.6 53.3 + - + +
118B LEU 4.3 0.2 - - - -
119B VAL* 1.3 71.7 - - - +
121B TYR* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY* 3.0 6.2 - - - -
73B TRP 2.9 34.2 + - - +
75B LEU* 4.1 9.2 - - + -
93B PHE* 2.6 34.1 + - - +
96B TYR* 3.7 1.3 - - + -
97B GLY* 3.1 52.3 - - - -
98B GLU 3.7 5.4 - - - -
99B ILE* 4.0 7.4 - - + -
100B LYS* 4.0 2.9 - - - -
119B VAL* 4.0 18.6 - - + -
120B GLU* 1.3 75.3 - - - +
122B GLU* 1.3 62.1 + - - +
123B THR 4.0 12.6 - - - +
126B GLU* 3.7 11.0 - - + +
127B ALA* 3.6 21.1 - - + +
130B ALA* 3.2 34.0 - - + +
----------------------------------------------------------
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