Contacts of the strand formed by residues 97 - 102 (chain D) in PDB entry 3M4D
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 GLN 97 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LYS* 4.0 17.2 + - - -
90D LEU* 4.0 1.3 - - - -
95D VAL 3.7 10.1 + - - +
96D ALA* 1.3 80.9 - - - +
98D ILE* 1.3 70.3 + - - +
162D ASP* 3.5 30.6 + - + +
163D LYS* 5.5 2.5 - - - +
232D ILE* 3.2 8.9 - - - -
233D THR* 2.8 44.8 + - - +
26E VAL* 3.1 42.6 + - + +
27E THR* 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LEU* 4.3 5.8 - - + +
90D LEU* 4.1 13.2 - - + -
97D GLN* 1.3 72.8 - - - +
99D SER* 1.3 59.7 + - - +
100D ASP 4.4 4.0 - - - +
101D TYR* 3.8 28.9 - - + -
161D THR 3.6 16.2 - - - +
162D ASP* 3.0 12.5 + - - +
163D LYS 3.4 3.8 - - - +
164D LYS* 3.2 45.5 - - - +
165D VAL* 3.5 18.4 - - + +
230D THR* 5.4 4.0 - - - +
231D VAL 3.7 5.4 - - - +
232D ILE* 4.6 9.4 - - + +
245D ILE* 5.9 1.6 - - + -
26E VAL* 3.6 9.4 - - - +
35E HIS* 2.9 20.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
97D GLN 3.4 0.4 + - - -
98D ILE* 1.3 74.0 - - - +
100D ASP* 1.3 60.2 + - - +
101D TYR* 4.7 0.5 - - - -
231D VAL* 2.8 18.6 + - - +
233D THR* 3.4 29.4 - - - +
24E ASP* 3.2 11.4 + - - -
26E VAL* 3.8 13.9 - - - +
35E HIS* 3.7 12.6 - - - -
37E LYS* 2.8 43.7 + - - +
59E GLY 5.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ASP 3.6 4.2 - - - +
5C ILE* 3.6 13.9 - - + +
6C ASN* 3.9 3.1 - - - +
98D ILE* 3.9 1.4 - - - +
99D SER* 1.3 79.4 - - - +
101D TYR* 1.3 94.6 + - - +
104D ARG* 2.8 25.8 + - - -
230D THR* 3.6 2.1 - - - -
231D VAL* 2.9 45.5 + - + +
37E LYS* 3.9 9.3 + - - +
58E LYS* 2.7 34.1 + - - +
59E GLY 5.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.5 4.4 - - - +
98D ILE* 3.8 15.3 - - + -
100D ASP* 1.3 100.8 + - - +
102D TYR* 1.3 64.6 + - - +
103D PRO 4.5 0.9 - - - -
104D ARG* 3.0 39.1 + - - +
157D LEU* 3.7 22.9 - - + -
160D PRO* 3.4 15.3 - - + +
165D VAL* 3.8 15.9 - - + -
167D TRP* 3.8 15.7 - - + -
229D ALA 3.1 12.6 - - - +
230D THR* 4.2 2.0 - - - +
35E HIS* 2.7 41.2 + + - -
59E GLY* 3.1 13.8 - - - -
60E THR* 2.7 29.1 + - - -
225E SER* 4.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ALA 3.5 18.6 - - - +
4C ASP* 3.2 42.8 + - + -
5C ILE* 4.2 15.3 - - + -
101D TYR* 1.3 75.5 - - - +
103D PRO* 1.3 94.8 - - + +
104D ARG* 3.6 26.0 - - + -
167D TRP* 3.6 3.9 - - - -
227D ASP 4.5 0.5 - - - +
228D PHE* 3.6 0.3 - - - -
229D ALA* 2.9 38.8 + - + +
----------------------------------------------------------
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