Contacts of the strand formed by residues 107 - 113 (chain V) in PDB entry 3SDI
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 GLY 107 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104V VAL* 3.3 2.6 - - - -
105V ASP 3.0 32.9 + - - -
106V THR* 1.3 80.3 - - - +
108V SER* 1.3 61.0 + - - -
109V HIS* 3.3 10.0 - - - -
180V ILE* 4.3 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7V LYS* 3.3 25.5 + - - +
8V PHE 4.9 1.4 + - - -
11V GLY* 3.8 39.0 + - - -
12V VAL* 4.5 1.8 - - - -
103V GLY 3.6 5.2 - - - -
104V VAL* 4.0 8.3 - - - -
107V GLY* 1.3 72.0 - - - -
109V HIS* 1.3 73.3 + - - +
180V ILE* 4.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 109 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7V LYS* 3.9 6.2 + - - +
12V VAL* 4.0 4.2 - - - +
76V VAL* 3.8 18.2 - - + -
77V VAL* 4.9 10.4 - - + +
102V ALA* 3.3 6.5 - - - +
103V GLY 2.9 27.7 + - - +
105V ASP* 3.2 21.2 + - - -
106V THR* 3.1 33.9 + - - -
107V GLY 3.3 24.4 + - - -
108V SER* 1.3 79.0 + - - +
110V LEU* 1.3 61.6 + - - +
111V PHE* 3.5 30.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V GLY* 3.6 38.1 - - - +
6V VAL 4.2 0.2 - - - -
7V LYS* 3.8 20.4 - - + +
12V VAL* 4.1 5.4 - - + -
100V ILE* 3.9 17.5 - - + -
101V VAL 3.7 4.9 - - - +
102V ALA* 4.0 11.0 - - + -
109V HIS* 1.3 74.9 - - - +
111V PHE* 1.3 74.6 + - - +
121V VAL* 3.6 3.2 - - - +
122V GLY 3.4 37.0 + - - +
123V TYR 3.4 28.0 - - - +
124V TYR* 3.9 2.5 - - - +
125V LEU* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219M TYR 4.8 0.2 - - - -
220M GLY* 3.7 34.5 - - - -
76V VAL* 3.6 24.5 - - + -
77V VAL* 4.1 15.0 - - + -
80V LEU* 3.3 37.9 - - + -
100V ILE* 3.5 5.0 - - - +
101V VAL* 2.8 39.4 + - + +
109V HIS* 3.5 33.9 - + + -
110V LEU* 1.3 80.7 - - - +
112V SER* 1.3 58.0 + - - +
120V ASP 3.3 14.1 - - - +
121V VAL* 3.8 20.9 - - + -
125V LEU* 3.6 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99V LEU 3.3 8.3 - - - -
100V ILE* 4.4 8.3 - - - +
111V PHE* 1.3 73.4 - - - +
113V ILE* 1.3 63.9 + - - +
114V HIS* 4.4 9.2 + - - -
119V THR* 3.1 9.4 - - - -
120V ASP* 3.0 52.4 + - - +
125V LEU* 3.6 20.0 - - - +
127V LEU* 4.7 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80V LEU* 3.3 35.9 - - + +
83V LEU* 3.7 31.4 - - + -
84V LYS* 4.4 9.0 - - - -
87V LEU* 3.7 26.7 - - + -
97V ALA 4.2 0.8 - - - +
98V TYR* 3.4 4.3 - - - -
99V LEU* 2.8 46.0 + - + +
101V VAL* 4.1 10.1 - - + -
112V SER* 1.3 79.0 - - - +
114V HIS* 1.3 71.3 + - - +
117V GLY 4.8 0.9 - - - -
118V SER 3.3 11.2 - - - +
119V THR* 3.8 10.1 - - + -
127V LEU* 4.3 0.5 - - - +
----------------------------------------------------------
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