Contacts of the strand formed by residues 93 - 99 (chain D) in PDB entry 3C5C
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 ALA 93 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASN 3.3 2.8 + - - -
23D LEU* 3.4 20.1 - - + -
24D ALA 3.1 22.2 + - - -
91D ALA* 3.5 5.0 - - - +
92D HIS* 1.3 78.3 - - - +
94D PHE* 1.3 65.8 + - - +
127D ILE* 3.6 1.6 - - - -
128D PRO* 3.5 20.4 - - + +
130D LEU* 5.7 0.9 - - + -
179D ALA* 3.4 32.5 - - + +
182D GLU* 5.0 0.2 - - + -
183D ALA* 4.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ALA* 3.4 22.0 - - + +
26D LEU* 3.9 14.1 - - + -
87D TYR* 3.6 30.3 - + - -
88D LEU* 4.1 10.1 - - + -
91D ALA* 3.5 18.6 - - + -
93D ALA* 1.3 73.2 - - - +
95D LEU* 1.3 69.1 + - - +
96D VAL* 4.1 1.3 - - + -
116D LEU* 3.7 45.3 - - + -
127D ILE* 3.2 48.9 - - + -
128D PRO 3.0 11.9 + - - +
129D ALA* 3.2 4.4 - - + -
130D LEU* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.1 2.7 - - + -
24D ALA 3.0 7.6 + - - +
25D ILE* 3.4 35.1 - - + +
26D LEU* 2.8 28.1 + - - +
36D LEU* 6.3 0.2 - - + -
94D PHE* 1.3 71.6 - - - +
96D VAL* 1.3 60.5 + - - +
97D VAL* 4.0 0.7 - - - -
130D LEU* 3.4 32.1 - - + -
132D LEU* 4.0 26.5 - - + -
175D VAL* 4.2 4.0 - - + +
176D PHE* 3.5 36.6 - - + -
179D ALA* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.6 17.7 - - + +
94D PHE* 4.7 2.7 - - + -
95D LEU* 1.3 75.5 - - - +
97D VAL* 1.3 63.2 + - - +
109D SER* 3.7 37.0 - - - +
112D TYR* 4.0 15.0 - - + -
113D LEU* 3.7 25.4 - - + -
116D LEU* 4.0 20.4 - - + -
129D ALA* 4.8 1.3 - - + -
130D LEU 2.7 14.1 + - - +
131D LEU* 3.4 13.2 - - + +
132D LEU* 2.9 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 3.6 30.1 - - + -
26D LEU 2.9 12.0 + - - +
27D GLY* 3.5 19.6 - - - -
28D ARG 4.1 1.6 + - - -
31D ALA* 3.6 21.5 - - + +
32D GLY 4.6 1.8 - - - -
33D LYS* 4.2 8.5 - - + -
36D LEU* 3.9 21.1 - - + -
95D LEU 4.3 1.6 - - - +
96D VAL* 1.3 75.2 - - - +
98D TYR* 1.3 73.5 + - - +
105D SER 4.7 0.9 - - - +
109D SER* 4.6 5.5 - - - -
132D LEU* 3.4 16.6 - - + +
134D ASN* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ALA* 3.9 8.1 - - - -
97D VAL* 1.3 72.8 - - - +
99D SER* 1.3 66.9 + - - +
100D VAL* 4.1 12.3 - - + -
105D SER* 3.3 30.7 - - - +
106D PHE* 3.7 35.2 - + + -
109D SER* 3.8 4.3 - - - -
131D LEU* 3.7 35.7 - - + -
132D LEU 3.0 9.5 + - - +
133D GLY* 3.5 21.5 - - - -
134D ASN* 2.7 36.0 + - - +
144D VAL* 3.9 14.1 - - + +
145D THR 4.6 0.3 + - - -
149D GLY* 3.4 13.9 + - - -
160D PHE* 3.2 22.7 - + - -
162D GLU* 4.5 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLY 4.7 1.2 + - - -
31D ALA* 3.9 7.9 - - - +
98D TYR* 1.3 78.8 - - - +
100D VAL* 1.3 58.3 + - - +
101D ASP* 3.0 23.7 + - - -
102D SER* 2.9 38.5 + - - +
105D SER* 2.8 17.4 + - - -
134D ASN 3.3 3.8 - - - -
135D LYS* 3.5 31.6 + - - -
144D VAL* 4.4 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