Contacts of the strand formed by residues 111 - 119 (chain A) in PDB entry 4ERO
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 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.1 3.8 - - + -
46A LYS* 3.3 5.9 - - - -
47A GLY 2.7 41.1 + - - +
48A GLY* 4.3 0.4 - - - -
67A LEU* 4.3 0.7 - - + -
71A GLY* 3.7 12.8 - - - +
72A SER 3.9 12.8 - - - +
73A MET* 3.7 37.2 - - + -
105A PRO* 4.2 2.6 - - + +
109A GLU 3.6 2.4 + - - -
110A PRO* 1.3 75.0 - - - +
112A HIS* 1.3 61.1 + - - +
113A GLY 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 2.7 38.2 + - + +
45A PHE 3.2 17.9 - - - -
46A LYS* 4.2 25.5 + - + +
67A LEU* 3.6 7.3 - - - +
68A LEU* 2.7 50.5 + - + +
69A GLU 3.6 22.0 + - - +
70A GLY* 5.0 0.2 - - - -
71A GLY 4.6 2.8 + - - +
110A PRO 4.0 0.8 + - - +
111A ALA* 1.3 75.5 - - - +
113A GLY* 1.3 54.2 + - - +
197A ILE* 4.3 15.7 - - + -
1002A EDO 5.2 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 3.5 6.8 - - - +
45A PHE* 2.9 40.8 + - - +
66A TYR 3.5 10.5 - - - -
67A LEU* 4.1 10.0 - - - +
68A LEU* 4.2 3.8 - - - -
111A ALA 4.2 0.2 - - - -
112A HIS* 1.3 75.4 - - - +
114A LEU* 1.3 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 3.8 26.5 - - + -
43A ASP 3.2 8.5 - - - +
44A GLU* 4.1 16.2 - - + -
45A PHE* 6.2 0.2 - - - -
64A VAL 3.3 4.2 - - - +
65A SER* 3.6 2.6 - - - -
66A TYR* 2.8 44.7 + - + +
68A LEU* 3.7 25.6 - - + -
113A GLY* 1.3 79.5 - - - +
115A GLN* 1.3 60.8 - - - +
171A TYR* 3.5 24.4 + - - +
195A TYR* 4.3 9.6 - - + -
197A ILE* 4.7 3.6 - - + -
239A VAL* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.6 2.9 - - + +
42A PHE* 3.1 9.3 - - - -
43A ASP* 2.7 41.3 + - + +
45A PHE* 5.6 2.8 - - + +
63A THR* 3.8 13.6 + - - -
64A VAL 3.5 4.2 - - - +
65A SER* 2.7 33.1 + - - +
103A GLU* 3.3 13.5 + - - +
114A LEU* 1.3 73.7 - - - +
116A LEU* 1.3 64.0 + - - +
117A TRP* 2.9 32.5 + - + +
1001A CO 4.1 11.8 + - - -
1005A EDO 3.8 29.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 4.5 4.3 - - + -
39A PHE* 3.6 31.2 - - + -
41A LEU 3.3 9.2 - - - +
42A PHE* 3.5 20.9 - - + -
63A THR* 3.5 1.9 - - - -
64A VAL* 2.9 41.0 + - + +
92A TRP* 5.7 0.2 - - + -
115A GLN* 1.3 77.0 - - - +
117A TRP* 1.3 72.4 + - - +
118A VAL* 3.9 21.3 + - + -
169A THR* 4.6 4.9 - - + -
171A TYR* 4.2 22.9 - - + +
193A PHE* 4.8 0.4 - - + -
241A ILE* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.4 6.1 - - - -
40A LEU* 2.9 44.8 + - + -
41A LEU* 2.8 50.7 + - + +
58A HIS* 3.5 28.5 - + - -
61A PHE* 3.5 27.1 - + - -
62A GLU 3.3 4.3 - - - +
63A THR* 3.7 12.2 - - + +
115A GLN* 2.9 29.9 + - + +
116A LEU* 1.3 85.3 - - - +
118A VAL* 1.3 61.6 - - - +
252A GLN* 4.0 24.2 - - - -
254A GLY 4.2 8.1 - - - -
255A PRO* 4.9 3.8 - - + -
1005A EDO 3.8 20.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO 3.5 6.5 - - - +
39A PHE* 4.6 6.7 - - + -
40A LEU* 4.2 0.2 - - - -
61A PHE* 3.2 2.0 - - - +
62A GLU* 2.7 57.6 + - + +
64A VAL* 4.1 20.0 - - + -
92A TRP* 4.5 6.5 - - + -
116A LEU* 3.9 26.2 - - + -
117A TRP* 1.3 73.7 - - - +
119A ASN* 1.3 73.4 + - - +
167A THR* 3.9 17.0 - - + +
169A THR* 3.7 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN* 5.7 0.2 - - - +
37A ASP* 5.7 1.2 + - - -
38A PRO* 2.7 22.1 + - + +
40A LEU* 3.8 24.0 - - + +
60A GLY 3.6 1.9 - - - +
61A PHE* 3.8 6.4 - - - +
62A GLU* 5.3 0.3 - - - +
118A VAL* 1.3 77.0 - - - +
120A LEU* 1.3 57.7 + - - +
125A LYS* 2.6 33.6 + - - +
167A THR* 2.7 31.0 + - - +
246A LEU* 3.6 19.5 - - + +
249A PRO 5.3 1.6 + - - -
250A VAL* 3.9 26.9 - - - +
257A VAL* 3.5 9.8 - - - +
258A MET 5.7 0.2 + - - -
259A ASN* 5.6 0.6 - - - +
----------------------------------------------------------
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