Contacts of the strand formed by residues 69 - 74 (chain D) in PDB entry 3EGC
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 69 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.6 6.5 - - + -
122C ARG* 3.4 32.5 - - - +
67D SER* 3.2 15.6 - - - +
68D ASN* 1.3 81.4 - - - +
70D VAL* 1.3 65.1 + - - +
99D SER* 3.4 10.1 - - - +
101D LEU* 3.9 24.7 - - + +
123D ARG 5.3 0.4 - - - +
124D VAL* 3.3 21.4 - - + -
125D ASP* 2.6 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D VAL* 1.3 81.5 - - - +
71D GLY* 1.3 71.8 + - - +
72D LEU* 3.9 0.8 + - - +
89D VAL* 5.5 0.2 - - + -
98D TYR* 3.9 15.7 - - + -
99D SER 2.9 11.7 + - - +
100D VAL* 3.5 5.8 - - + -
101D LEU* 2.9 26.2 + - - +
124D VAL* 4.1 4.3 - - - -
126D GLY 3.5 5.8 - - - +
128D ILE* 4.8 2.0 - - + -
308D MET* 3.6 31.2 - - + -
311D LEU* 3.6 35.0 - - + -
312D ILE* 5.7 0.2 - - + -
315D ILE* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D VAL* 1.3 77.2 - - - +
72D LEU* 1.3 60.8 + - - -
73D ILE 4.0 0.4 - - - -
101D LEU* 3.7 3.4 - - - -
119D PHE* 3.6 23.6 - - - -
124D VAL* 3.8 7.0 - - - +
126D GLY 3.0 10.9 + - - -
127D LEU* 3.3 12.2 - - - +
128D ILE 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 5.0 3.1 - - + -
70D VAL* 3.9 1.3 + - + -
71D GLY* 1.3 72.1 - - - -
73D ILE* 1.3 60.0 + - - +
74D VAL* 3.7 24.7 - - + -
85D VAL* 5.4 2.9 - - + -
86D ALA* 3.7 35.4 - - + +
89D VAL* 4.3 18.4 - - + -
100D VAL* 3.8 20.0 - - + -
101D LEU 2.7 16.5 + - - +
102D LEU* 3.5 15.1 - - + -
103D ALA 2.8 32.6 + - - +
119D PHE* 3.7 1.9 - - - -
128D ILE* 3.5 31.2 - - + +
130D ALA 5.6 0.4 - - - +
152D VAL* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLY 4.8 0.7 - - - -
72D LEU* 1.3 77.0 - - - +
74D VAL* 1.3 65.8 + - - +
103D ALA* 3.6 4.9 - - + +
105D THR* 3.8 26.0 - - + -
112D GLU* 4.4 5.2 - - + +
115D ALA* 3.8 12.8 - - + -
116D VAL* 3.5 44.9 - - + +
119D PHE* 3.7 22.2 - - + -
127D LEU* 4.1 11.4 - - + -
128D ILE 2.9 11.3 + - - +
129D LEU* 3.6 22.2 - - + -
130D ALA* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LEU* 3.7 31.0 - - + -
73D ILE* 1.3 80.0 - - - +
75D SER* 1.3 63.8 + - - +
76D ASP 3.4 13.2 - - - +
77D ILE* 3.4 30.7 - - + +
82D PHE* 3.6 29.8 - - + +
85D VAL* 5.6 4.0 - - + -
86D ALA* 5.1 0.9 - - + -
102D LEU* 4.9 1.3 - - + -
103D ALA 3.0 11.8 + - - +
104D ASN* 3.6 2.5 - - - +
105D THR* 3.1 26.4 + - - +
130D ALA* 3.8 11.7 - - + -
152D VAL* 5.9 0.7 - - + -
----------------------------------------------------------
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