Contacts of the strand formed by residues 70 - 74 (chain C) in PDB entry 3SRF
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 70 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY* 6.3 0.4 - - - -
46C ILE 3.2 3.4 + - - +
47C ILE* 3.4 33.0 - - + -
48C CYS 2.8 29.1 + - - +
68C MET* 4.0 5.4 - - - +
69C ASN* 1.3 85.9 - - + +
71C ALA* 1.3 61.1 + - - +
72C ARG 3.5 0.3 + - - -
108C ALA* 3.5 23.8 - - + +
110C ALA* 3.7 27.8 - - + -
238C MET* 4.2 13.7 - - + -
240C PHE* 4.7 0.7 - - + -
357C CYS* 5.7 1.3 - - - -
463C HIS* 4.0 20.9 - - + +
464C LEU* 5.3 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C CYS 3.3 5.4 - - - -
50C ILE* 4.0 21.5 - - + -
68C MET* 4.3 9.4 - - - -
70C VAL* 1.3 69.6 - - - +
72C ARG* 1.3 62.8 + - - +
73C LEU* 3.7 8.1 + - + +
90C VAL* 4.1 27.4 - - + -
107C VAL* 4.1 2.9 - - + +
108C ALA 2.7 14.7 + - - +
109C VAL* 3.7 4.0 - - + -
110C ALA* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 3.8 13.2 - - + -
48C CYS 2.6 16.1 + - - +
49C THR* 3.1 38.9 + - + +
50C ILE 3.0 27.4 + - - -
70C VAL 3.5 2.0 + - - -
71C ALA* 1.3 72.8 - - - +
73C LEU* 1.3 65.9 + - - +
74C ASN* 4.0 21.9 + - - +
110C ALA* 3.6 7.4 - - - +
112C ASP* 2.6 49.2 + - + -
240C PHE* 4.1 8.5 - - + -
269C LYS* 3.9 2.6 - - - +
359C MET* 3.5 28.2 - - - +
361C SER* 3.4 16.8 - - - -
532C K 4.1 1.4 - - - -
534C PYR 3.6 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 4.8 7.4 - - + +
71C ALA* 3.9 18.2 - - + +
72C ARG* 1.3 81.7 - - - +
74C ASN* 1.3 62.9 + - - +
75C PHE* 3.4 16.3 + - + -
83C HIS* 3.7 31.6 - - + +
86C THR* 4.6 18.8 - - + -
87C ILE* 3.4 34.1 - - + +
90C VAL* 5.4 3.1 - - + -
109C VAL* 4.4 14.4 - - + -
110C ALA 2.8 15.8 + - - +
111C LEU* 4.9 0.2 - - - -
112C ASP* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C THR* 5.1 7.8 - - - +
50C ILE 5.1 7.0 + - - +
72C ARG* 4.0 23.1 + - - +
73C LEU* 1.3 70.8 - - - +
75C PHE* 1.3 58.4 + - - +
76C SER* 3.1 25.1 + - - -
77C HIS* 3.2 39.8 + - + +
83C HIS* 3.0 21.8 - - - -
112C ASP* 4.3 3.5 - - - +
532C K 3.4 10.6 - - - -
----------------------------------------------------------
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