Contacts of the strand formed by residues 122 - 130 (chain A) in PDB entry 5C16
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 ALA 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET* 4.7 12.4 - - + +
115A TYR 3.2 11.4 - - - +
116A ILE* 4.3 14.6 - - + -
117A CYS 4.5 0.7 - - - +
120A MET 3.4 4.2 + - - -
121A GLY* 1.3 75.3 - - - +
123A VAL* 1.3 65.2 + - - +
124A SER 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL 3.6 0.2 - - - +
114A MET* 3.1 10.2 - - - +
115A TYR* 2.9 31.6 + - + +
117A CYS* 4.3 23.1 - - - -
120A MET 5.1 3.4 - - - +
122A ALA* 1.3 77.4 - - - +
124A SER* 1.3 74.5 + - - +
136A PHE* 4.1 3.5 - - + -
138A ASN* 3.8 22.7 - - + +
145A PHE* 4.1 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 5.2 7.0 - - - -
113A VAL 3.6 4.0 - - - -
114A MET* 3.6 23.6 - - - -
122A ALA 4.2 0.6 + - - -
123A VAL* 1.3 76.5 - - - +
125A GLY* 1.3 55.8 + - - +
136A PHE* 3.8 2.5 - - - -
138A ASN* 2.3 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 3.1 7.9 + - - +
113A VAL* 2.8 34.8 + - - +
124A SER* 1.3 77.0 - - - +
126A THR* 1.3 64.5 + - - -
136A PHE* 3.5 12.5 - - - -
137A LYS 3.2 13.5 - - - -
138A ASN* 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 3.7 26.9 - - + -
110A VAL 3.4 12.3 - - - +
111A LYS* 3.9 28.2 - - + +
112A ASP 4.6 0.3 + - - -
125A GLY* 1.3 74.0 - - - -
127A LEU* 1.3 61.3 + - - +
128A THR* 3.8 4.9 + - - +
135A TYR* 3.6 2.4 - - - +
136A PHE* 3.4 6.1 - - - -
137A LYS* 3.0 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 3.8 1.2 - - - +
109A ILE* 3.4 1.7 - - - -
110A VAL* 2.7 42.4 + - + +
113A VAL* 4.3 13.7 - - + -
125A GLY 4.1 1.4 + - - -
126A THR* 1.3 70.8 - - - +
128A THR* 1.3 67.9 + - - +
129A VAL* 4.0 13.7 + - + +
134A LEU* 4.3 17.9 - - + -
135A TYR 3.2 24.2 - - - +
136A PHE* 4.2 16.4 - - + -
184A LEU* 3.8 28.5 - - + -
196A ILE* 3.6 29.6 - - + -
200A LEU* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 3.8 28.0 + - + +
106A ILE* 3.8 26.7 - - + -
108A ALA 3.2 10.5 - - - +
109A ILE* 3.7 26.2 - - + +
126A THR* 3.8 5.4 + - - +
127A LEU* 1.3 76.0 - - - +
129A VAL* 1.3 62.6 + - - +
130A THR* 4.2 8.9 + - + +
133A LYS 4.2 0.3 - - - +
134A LEU* 3.4 2.9 - - - -
135A TYR* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 3.7 1.6 - - - +
107A LYS* 2.7 32.2 + - + +
108A ALA* 2.7 30.5 + - + +
110A VAL* 6.4 0.2 - - + -
127A LEU* 4.3 20.6 - - + +
128A THR* 1.3 76.2 - - - +
130A THR* 1.3 66.8 + - - +
133A LYS 3.9 4.5 - - - +
134A LEU* 4.6 1.3 - - + +
151A LEU* 4.6 8.1 - - + -
196A ILE* 5.4 5.8 - - + +
199A ASN* 4.5 22.4 - - + +
200A LEU* 4.4 29.6 - - + -
203A HIS* 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 5.6 0.9 - - + -
100A LEU* 3.8 17.3 - - + -
104A GLU* 2.5 33.4 + - - +
105A SER 3.2 15.5 - - - +
106A ILE* 4.3 2.5 - - + -
107A LYS* 3.8 5.6 - - - -
128A THR* 4.2 16.4 - - + +
129A VAL* 1.3 82.2 - - - +
131A ASP* 1.3 62.0 + - - +
132A PHE 2.7 13.0 + - - -
133A LYS* 2.9 25.6 + - + +
135A TYR* 5.8 0.4 - - + -
151A LEU* 3.2 18.5 - - - +
203A HIS* 4.1 2.4 - - - +
----------------------------------------------------------
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