Contacts of the strand formed by residues 154 - 158 (chain B) in PDB entry 3AP1
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 VAL 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 4.1 22.2 - - + +
71B ILE* 3.5 34.8 - - + -
93B GLU* 2.8 15.5 + - + +
94B VAL* 3.3 8.5 - - + +
95B ARG 3.1 24.4 + - - -
152B ALA* 3.8 2.1 - - - +
153B ARG* 1.3 114.8 - - - +
155B LEU* 1.3 67.3 + - - +
258B ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 3.5 23.3 - - + -
68B MET* 3.3 29.3 - - + +
69B PRO 3.7 5.9 + - - -
70B LEU* 3.3 24.6 - - + -
71B ILE 3.0 20.1 + - - -
95B ARG* 3.5 35.4 - - - +
145B ILE* 4.0 8.7 - - + -
146B ALA* 3.8 24.7 - - - -
150B GLU 4.1 0.2 - - - +
152B ALA* 3.9 25.1 - - + +
153B ARG 4.1 1.0 + - - -
154B VAL* 1.3 79.3 - - - +
156B CYS* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 5.1 1.3 - - - -
71B ILE* 3.1 25.1 - - + +
73B VAL* 4.0 20.0 - - - -
88B LEU* 4.2 2.2 - - - -
94B VAL* 4.0 9.2 - - + -
95B ARG* 2.8 16.5 + - - +
96B CYS* 2.0 67.6 - - - +
145B ILE* 4.2 6.1 - - - +
155B LEU* 1.3 77.2 - - - +
157B ASN* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 5.9 0.2 - - - +
71B ILE 2.8 6.9 + - - -
72B PHE* 3.5 16.2 - - + +
73B VAL 2.9 25.6 + - - +
96B CYS 4.7 1.1 - - - -
98B GLU 5.1 0.8 + - - -
100B THR* 3.3 31.3 - - - +
103B ILE* 3.5 19.1 - - - +
145B ILE* 3.8 23.9 - - + +
148B HIS* 4.3 6.9 + - - -
156B CYS* 1.3 78.7 + - - +
158B LYS* 1.3 61.3 + - - +
159B ASP* 3.0 24.9 + - - +
162B THR* 4.4 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A3P 4.3 0.2 + - - -
73B VAL* 3.5 33.0 - - + +
81B THR* 2.9 39.2 + - - +
82B THR* 2.8 29.2 + - - +
85B ARG* 3.7 27.6 - - + +
96B CYS* 4.8 5.2 + - + +
97B GLY 5.0 4.3 + - - +
98B GLU 4.3 2.4 + - - +
99B GLU* 2.8 52.2 + - - +
156B CYS* 4.7 0.8 - - - -
157B ASN* 1.3 76.3 - - - +
159B ASP* 1.3 71.6 + - - +
160B PRO* 3.8 8.7 - - + -
283B GLU* 4.6 1.1 + - - -
1006T TYR* 4.5 1.0 + - - -
----------------------------------------------------------
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