Contacts of the strand formed by residues 94 - 100 (chain G) in PDB entry 3SR2
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 THR 94 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ALA* 1.3 84.4 + - - +
95G PHE* 1.3 88.5 + - - +
109G ARG* 2.8 71.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G LEU* 3.9 18.6 - - + -
17G GLN 4.0 6.7 + - - +
18G LEU* 3.5 32.1 - - + +
19G ALA* 4.0 5.5 + - - +
79G LEU* 4.8 15.3 - - + -
80G LEU* 4.2 22.2 - - + -
83G LEU* 3.2 34.1 - - + -
93G ALA 5.1 4.5 - - - -
94G THR* 1.3 104.7 + - - +
96G SER* 1.3 63.2 + - - +
106G LEU* 5.5 3.8 - - + -
107G ARG 3.4 6.3 - - - +
108G VAL* 3.4 38.1 - - + -
109G ARG* 4.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G LEU* 3.9 6.5 - - - -
19G ALA* 4.5 11.4 - - - -
95G PHE* 1.3 75.5 - - - +
97G CYS* 1.3 62.0 + - - +
98G ASP* 5.2 2.2 - - - -
106G LEU* 4.0 3.5 - - - +
107G ARG* 3.0 62.4 + - - +
109G ARG* 5.1 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G LEU* 3.3 30.4 + - + -
19G ALA* 4.7 3.4 - - - +
21G ASN* 4.1 17.8 + - - +
23G LEU* 3.9 22.4 - - - -
96G SER* 1.3 74.5 - - - +
98G ASP* 1.3 68.8 + - - +
99G CYS* 4.4 8.1 + - - -
104G LEU* 3.5 34.5 - - - -
105G ILE 3.9 2.5 - - - -
106G LEU* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP* 5.1 12.5 - - - +
100C VAL* 5.0 6.9 - - + +
96G SER* 4.3 2.6 + - - -
97G CYS* 1.3 81.4 + - - +
99G CYS* 1.3 67.0 + - - +
100G VAL* 4.3 3.6 - - + -
104G LEU* 3.7 2.9 - - - +
105G ILE* 2.9 51.3 + - + +
107G ARG* 3.6 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP* 5.1 2.4 - - - +
107C ARG* 2.9 21.2 + - - -
21G ASN* 6.2 3.6 - - - -
45G TRP* 5.5 6.5 - - + -
97G CYS* 4.4 8.9 + - - -
98G ASP* 1.3 75.7 - - - +
100G VAL* 1.3 64.5 + - - +
103G ALA 4.2 6.7 - - - +
104G LEU* 3.3 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP* 4.0 21.5 - - + -
99C CYS* 4.5 1.3 - - - +
100C VAL* 3.5 47.9 - - + +
103C ALA 4.5 2.5 - - - +
105C ILE* 3.6 31.2 - - + +
107C ARG* 3.8 5.8 - - - +
98G ASP* 4.4 4.0 + - + +
99G CYS* 1.3 83.6 - - - +
101G ALA* 1.3 75.9 + - + +
103G ALA* 2.8 29.1 + - - +
105G ILE 5.5 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