Contacts of the strand formed by residues 155 - 163 (chain A) in PDB entry 3IVV
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 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP 3.5 2.4 - - - +
37A THR* 3.3 1.2 - - - -
38A ILE* 2.8 46.2 + - + +
41A PHE* 3.7 37.0 - - + +
84A LEU* 3.8 17.9 - - + -
106A ILE* 4.1 22.7 - - + -
142A LEU* 4.1 12.1 - - + -
149A LEU 4.3 0.9 - - - +
150A LEU* 3.7 21.0 - - + +
153A ASP 4.2 0.6 + - - -
154A LYS* 1.3 70.8 - - - +
156A THR* 1.3 63.0 + - - +
157A LEU* 4.0 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 3.7 29.4 - - + -
36A TRP 3.4 2.7 - - - +
37A THR* 2.8 32.5 + - - +
106A ILE* 3.4 8.0 - - - +
107A LEU* 2.9 58.9 + - + -
149A LEU 5.0 0.4 + - - -
151A PRO* 6.1 0.9 - - - +
154A LYS* 3.8 6.2 + - - +
155A LEU* 1.3 73.1 - - - +
157A LEU* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR 3.8 1.0 - - - +
35A MET* 3.4 6.2 - - - +
36A TRP* 2.8 63.6 + - + +
38A ILE* 4.5 6.5 - - + -
69A LEU* 4.9 8.5 - - + -
71A VAL* 4.7 6.5 - - + -
84A LEU* 5.2 2.7 - - + -
86A LEU* 3.9 42.2 - - + -
104A PHE* 5.6 0.2 - - + -
105A SER 3.5 3.6 - - - +
106A ILE* 4.1 15.3 - - + -
136A PHE* 4.5 3.8 - - + -
155A LEU* 4.0 37.0 - - + +
156A THR* 1.3 75.0 - - - +
158A PHE* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER* 3.6 21.3 - - - -
34A TYR 3.4 10.1 - - - -
35A MET* 3.9 36.6 - - + -
103A LYS* 3.6 2.0 + - - +
104A PHE* 3.3 6.5 - - - -
105A SER* 2.9 51.0 + - - +
107A LEU* 3.8 20.6 - - + -
113A GLU* 3.4 22.0 - - + -
157A LEU* 1.3 76.3 - - - +
159A CYS* 1.3 60.2 + - - +
160A GLU* 3.4 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE 3.7 1.4 - - - +
33A SER* 3.3 1.8 - - - -
34A TYR* 2.8 45.5 + - + +
57A PHE* 5.1 1.8 - - - -
69A LEU* 3.9 22.0 - - + -
88A LEU* 4.3 8.1 - - - -
102A PHE* 4.8 2.0 - - - -
103A LYS 3.3 7.2 - - - -
104A PHE* 3.6 35.7 - - + -
157A LEU 4.3 0.2 - - - -
158A PHE* 1.3 72.3 - - - +
160A GLU* 1.3 64.9 + - - +
161A VAL* 3.7 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE 3.4 4.7 - - - +
33A SER* 2.5 25.2 + - - +
102A PHE* 3.2 5.5 - - - +
103A LYS* 2.9 70.5 + - + +
113A GLU* 3.9 5.6 - - - +
158A PHE* 3.4 30.7 - - + -
159A CYS* 1.3 73.2 - - - +
161A VAL* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.2 5.9 - - - +
32A PHE* 2.8 72.9 + - + +
57A PHE* 4.9 2.0 - - + -
67A TRP* 4.6 2.7 - - + -
88A LEU* 3.8 23.3 - - + -
100A ALA* 4.0 19.5 - - + -
101A LYS 3.4 10.8 - - - +
102A PHE* 4.5 0.7 - - + -
159A CYS* 3.7 24.2 - - - +
160A GLU* 1.3 78.7 - - - +
162A SER* 1.3 66.1 + - - +
163A VAL* 4.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL 3.5 4.9 - - - -
31A LYS* 3.4 35.0 + - - +
100A ALA* 3.4 0.9 - - - -
101A LYS* 2.9 54.4 + - - +
161A VAL* 1.3 73.5 + - - +
163A VAL* 1.3 64.0 + - - +
164A VAL* 3.8 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL 5.6 1.3 - - - +
30A VAL* 2.9 18.4 + - - +
32A PHE* 3.8 25.8 - - + -
59A SER* 4.5 0.4 - - - +
65A LEU* 4.3 20.6 - - + -
67A TRP* 3.9 22.2 - - + -
98A VAL* 4.3 12.1 - - + -
99A ARG 3.6 10.1 - - - +
100A ALA* 4.0 7.2 - - + -
161A VAL* 4.3 0.2 - - + -
162A SER* 1.3 74.5 - - - +
164A VAL* 1.3 72.1 + - - +
165A GLN* 2.9 31.2 + - - +
----------------------------------------------------------
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