Contacts of the strand formed by residues 124 - 135 (chain A) in PDB entry 2FE3
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 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET 5.8 2.4 + - - -
118A ALA* 5.4 0.2 - - - -
122A GLY 3.8 2.6 + - - +
123A PHE* 1.3 73.2 - - - +
125A VAL* 1.3 61.8 + - - +
134B GLY* 3.1 5.4 - - - -
135B VAL* 2.9 43.8 + - + +
140B SER* 2.7 31.2 + - - +
143B GLU* 5.6 1.8 + - - -
145B HIS* 2.6 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A HIS* 6.0 0.5 + - - -
85A ASP* 5.8 0.2 - - - +
114A GLU* 3.5 53.6 - - + +
117A ALA* 5.3 1.6 - - + -
118A ALA* 4.0 18.5 - - + +
123A PHE* 3.9 7.2 + - + +
124A LYS* 1.3 73.6 - - - +
126A SER* 1.3 63.7 + - - +
127A HIS 4.0 3.8 - - - +
132B ILE* 3.4 33.0 - - + -
133B TYR 3.9 3.1 - - - -
134B GLY* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE 5.5 1.7 + - - -
88A THR* 3.8 19.9 + - - +
90A ASP* 4.8 0.2 - - - +
114A GLU* 4.8 2.1 - - - +
124A LYS 3.8 1.6 + - - -
125A VAL* 1.3 75.9 - - - +
127A HIS* 1.3 82.6 + - - +
97B GLU* 3.9 13.5 + - - -
133B TYR 2.8 15.1 + - - -
134B GLY* 4.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 3.4 36.6 - - + +
89A SER 3.7 15.0 - - - +
90A ASP* 3.3 16.2 - - - +
91A HIS* 5.8 2.7 - + - -
114A GLU* 4.1 6.1 - - - -
125A VAL* 4.0 1.6 - - - +
126A SER* 1.3 100.2 + - - +
128A HIS* 1.3 69.1 + - - +
97B GLU* 3.2 31.7 + - - -
132B ILE* 3.7 2.9 - - - +
133B TYR* 2.8 55.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER 4.5 1.2 - - - +
90A ASP* 2.9 37.3 + - + -
91A HIS* 3.1 23.1 + - - +
92A TYR* 2.8 36.7 + + - -
109A GLY* 4.4 0.9 - - - -
110A LEU* 3.5 41.8 - - + +
114A GLU* 2.7 28.3 + - - +
127A HIS* 1.3 78.4 - - - +
129A ARG* 1.3 63.5 + - - +
130A LEU 4.7 0.9 - - - -
130B LEU* 4.0 11.4 - - + -
131B GLU 3.1 14.1 - - - +
132B ILE* 4.2 9.9 - - + -
133B TYR* 4.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A HIS* 3.3 19.7 - - + +
93A HIS* 4.1 19.6 + - + +
127A HIS* 6.2 0.2 - - + -
128A HIS* 1.3 74.4 - - - +
130A LEU* 1.3 60.9 + - - +
131A GLU* 3.2 30.1 + - - -
129B ARG* 2.7 32.3 - - - +
130B LEU* 3.6 4.3 - - - +
131B GLU* 2.6 62.9 + - - +
133B TYR* 4.1 22.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A HIS 2.9 6.9 + - - +
92A TYR* 3.4 25.7 - - + -
93A HIS* 2.9 28.6 + - - +
105A PHE* 4.7 1.3 - - + -
110A LEU* 4.6 7.4 - - + -
128A HIS* 4.3 0.8 - - + -
129A ARG* 1.3 73.0 - - - +
131A GLU* 1.3 63.7 + - - +
132A ILE* 4.0 17.0 - - + -
110B LEU* 3.7 28.9 - - + -
113B VAL* 3.5 33.2 - - + -
128B HIS* 4.1 14.4 - - + -
129B ARG 3.7 13.5 - - - +
130B LEU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS* 3.5 10.6 + - + +
95A ILE* 3.9 19.7 - - + +
129A ARG* 3.2 36.8 + - + -
130A LEU* 1.3 72.3 - - - +
132A ILE* 1.3 62.0 + - - +
133A TYR* 2.3 41.8 + - + +
128B HIS* 3.2 5.7 - - - +
129B ARG* 2.7 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS 2.8 16.4 + - - +
94A ALA* 3.3 9.0 - - + +
95A ILE* 2.8 31.8 + - - +
105A PHE* 3.7 12.3 - - + -
130A LEU* 4.0 23.3 - - + -
131A GLU* 1.3 76.0 - - - +
133A TYR* 1.3 60.5 + - - +
113B VAL* 4.2 7.6 - - + -
114B GLU* 4.3 14.6 - - + -
117B ALA* 3.6 28.5 - - + -
123B PHE* 5.0 2.3 - - + -
125B VAL* 3.5 39.5 - - + -
127B HIS 3.7 5.4 - - - +
128B HIS* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.5 36.6 - - + +
97A GLU* 4.0 12.8 - - + -
131A GLU* 2.3 51.4 + - + -
132A ILE* 1.3 74.7 - - - +
134A GLY* 1.3 59.3 + - - +
123B PHE* 5.3 0.4 - - - -
125B VAL* 3.8 3.6 - - - +
126B SER* 2.8 23.7 + - - -
127B HIS* 2.7 60.4 + + + +
128B HIS* 4.4 1.1 - - - -
129B ARG* 3.8 25.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE 3.1 8.9 + - - -
96A CYS* 3.4 1.9 - - - -
97A GLU* 2.8 34.0 + - - +
132A ILE 4.1 0.4 + - - -
133A TYR* 1.3 76.0 - - - +
135A VAL* 1.3 66.2 + - - +
123B PHE* 4.2 6.8 - - - -
124B LYS 3.1 14.1 - - - -
125B VAL* 4.4 0.4 - - - -
126B SER* 3.9 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A CYS* 3.9 2.7 - - - -
97A GLU* 5.2 3.1 - - + +
98A ASN* 3.9 27.8 - - - +
134A GLY* 1.3 80.8 - - - +
136A CYS* 1.3 70.4 + - - +
139A CYS* 3.5 26.7 - - + -
140A SER* 3.6 15.4 - - - +
143A GLU* 4.6 4.5 - - - +
123B PHE* 3.3 4.7 - - - -
124B LYS* 2.8 43.0 + - + +
----------------------------------------------------------
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