Contacts of the strand formed by residues 73 - 78 (chain A) in PDB entry 5A31
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 SER 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS 4.6 4.2 + - - -
72A GLU* 1.3 78.3 - - - +
74A TRP* 1.3 75.9 + - - +
94A TYR* 3.6 3.1 - - - -
95A VAL* 3.0 41.2 + - - +
125A GLN 5.6 0.9 + - - -
588A ARG* 4.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 4.1 10.4 - + - -
22A PRO* 3.8 19.7 - - + -
25A ARG* 4.1 24.2 - - - -
72A GLU* 4.1 19.3 - - - -
73A SER* 1.3 88.9 + - - +
75A GLN* 1.3 66.1 + - - +
76A LEU* 4.0 13.0 - - + -
92A GLU* 5.4 1.8 - - + -
93A LEU 3.3 14.8 - - - +
94A TYR* 3.7 26.7 - + + -
95A VAL* 5.5 0.2 - - - -
588A ARG* 2.9 41.7 + - - +
589A ASP* 2.8 33.3 + - - +
604A MET* 3.4 36.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 1.3 76.4 - - - +
76A LEU* 1.3 73.6 + - - +
91A GLU 3.8 0.2 - - - +
92A GLU* 3.3 0.7 - - - -
93A LEU* 3.0 42.1 + - + +
125A GLN* 4.6 8.1 + - - -
126A ALA 4.2 5.1 + - - -
127A LEU* 4.1 30.8 - - - +
128A TRP* 4.1 17.4 + - + -
589A ASP* 4.1 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 4.4 8.3 - - + -
74A TRP* 4.0 18.4 - - + -
75A GLN* 1.3 93.1 - - - +
77A ARG* 1.3 63.4 + - - +
90A ASP* 4.0 10.1 - - + -
91A GLU 3.1 13.0 - - - +
92A GLU* 3.7 21.1 - - + -
106A SER* 4.0 17.5 - - - +
128A TRP* 4.1 3.1 - - - -
589A ASP* 4.1 20.2 + - + +
591A VAL* 4.3 14.3 - - + +
606A ARG* 3.6 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 1.3 77.2 - - - +
78A LYS* 1.3 76.2 + - + +
79A ALA 3.2 2.8 + - - -
80A VAL* 3.9 20.8 - - - +
90A ASP* 3.5 8.0 - - - +
91A GLU* 2.6 50.5 + - - +
102A TRP* 4.4 6.5 - - - -
128A TRP* 3.3 66.2 - - + +
129A CYS 5.4 3.2 + - - +
149A LYS* 6.0 8.1 - - - +
164A ILE* 6.0 2.0 - - - +
591A VAL* 3.6 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 1.3 89.0 + - + +
79A ALA* 1.3 73.8 + - - +
80A VAL* 3.9 5.1 + - + +
86A ASP 5.2 0.8 + - - -
87A VAL* 3.8 9.2 - - + +
88A ASP* 3.4 26.6 - - - +
89A TYR 4.1 4.5 - - - +
483A GLU* 4.6 13.5 - - - +
591A VAL* 3.4 15.6 - - + +
592A HIS* 3.0 59.1 + - + +
594A ARG* 5.5 0.9 - - - +
----------------------------------------------------------
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