Contacts of the strand formed by residues 73 - 82 (chain P) in PDB entry 2P4E
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 ARG 73 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P ARG* 3.6 41.2 - - - +
67P CYS* 3.5 34.8 - - + +
69P LYS 4.0 1.3 - - - +
70P ASP* 3.0 45.8 + - - +
71P PRO 4.3 4.7 - - - +
72P TRP* 1.3 82.5 - - - +
74P LEU* 1.3 68.1 + - - +
75P PRO* 3.6 24.2 - - + +
145P GLU* 2.8 40.0 + - - +
146P ASP 4.1 2.5 - - - -
147P SER* 4.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PRO* 5.8 1.8 - - + -
258A LYS* 5.6 4.9 - - - +
259A GLY 5.1 0.2 - - - +
260A THR* 3.5 32.8 - - + -
73P ARG* 1.3 80.5 - - - +
75P PRO* 1.3 72.5 - - - +
77P THR* 3.7 16.0 + - - +
145P GLU* 3.9 1.2 - - - +
146P ASP* 2.9 29.7 + - + +
147P SER* 3.7 21.5 - - - +
148P SER* 3.9 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P ARG* 3.6 25.4 - - + +
74P LEU* 1.3 93.0 - - - +
76P GLY* 1.3 59.5 + - - +
77P THR* 5.0 0.5 + - - -
78P TYR* 4.8 3.4 - - - +
145P GLU* 3.2 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P PRO* 1.3 74.0 - - - +
77P THR* 1.3 61.7 + - - +
78P TYR* 3.9 13.6 + - - -
125P LYS* 3.4 10.4 - - - +
126P MET 3.1 41.7 + - - +
127P SER* 5.5 0.9 - - - -
128P GLY 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P LEU* 3.7 5.7 + - - +
75P PRO 3.4 4.1 + - - -
76P GLY* 1.3 80.5 + - - +
78P TYR* 1.3 68.3 + - - +
112P LEU* 4.0 13.5 - - + +
123P LEU* 3.4 32.1 - - + -
124P VAL 3.3 10.1 - - - +
125P LYS* 4.3 10.0 - - - +
145P GLU* 3.8 1.7 - - - +
146P ASP* 2.9 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P PHE* 3.7 28.7 - + - -
75P PRO* 4.7 1.9 - - - +
76P GLY* 3.9 21.1 + - - -
77P THR* 1.3 75.9 - - - +
79P VAL* 1.3 64.0 + - - +
80P VAL* 3.7 0.6 + - + -
123P LEU* 3.5 4.9 - - - -
124P VAL* 2.8 46.7 + - + +
126P MET* 3.5 42.8 - - + -
128P GLY* 3.4 23.8 + - - -
131P LEU* 3.8 19.1 - - + +
143P ILE* 3.9 13.2 - - + -
144P GLU 3.5 1.3 - - - -
145P GLU* 3.6 35.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 5.5 1.3 - - + -
262A SER* 4.3 9.9 - - - +
265A LEU* 4.1 20.9 - - + -
296A VAL* 4.0 21.3 - - + -
78P TYR* 1.3 70.7 - - - +
80P VAL* 1.3 62.4 + - - +
81P VAL* 3.6 23.3 + - + +
115P PHE* 4.3 13.2 - - + -
122P PHE 3.6 7.2 - - - +
123P LEU* 3.6 22.2 - - + -
143P ILE* 3.3 4.5 - - - -
144P GLU* 2.8 43.0 + - + +
146P ASP* 4.9 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P TYR 4.4 0.2 - - - +
79P VAL* 1.3 74.1 - - - +
81P VAL* 1.3 62.8 + - - +
82P LEU* 4.0 5.2 - - + -
98P LEU* 4.9 3.6 - - + -
115P PHE* 5.3 0.2 - - - -
121P GLY* 3.1 7.3 - - - -
122P PHE* 2.8 76.9 + - + +
124P VAL* 4.0 16.6 - - + -
126P MET* 5.7 0.7 - - + -
134P ALA* 5.3 2.0 - - + -
137P LEU* 5.4 1.6 - - + -
140P VAL* 3.9 29.2 - - + -
142P TYR 3.9 2.0 - - - -
143P ILE* 4.1 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 3.5 31.4 - - + -
79P VAL* 3.8 12.6 - - + +
80P VAL* 1.3 74.1 - - - +
82P LEU* 1.3 66.4 + - - +
119P LEU* 4.6 18.2 - - + -
120P PRO* 3.8 9.2 - - + +
140P VAL* 3.7 2.3 - - - +
141P ASP* 2.7 32.0 + - + +
142P TYR* 2.8 59.4 + - + +
144P GLU 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P VAL* 4.0 10.3 - - + -
81P VAL* 1.3 88.7 - - - +
83P LYS* 1.3 66.4 + - - +
84P GLU* 3.6 1.0 + - - -
86P THR* 3.7 22.7 - - + +
91P SER* 3.4 41.3 - - - +
94P THR* 4.3 13.9 - - + +
120P PRO* 3.0 21.2 + - - +
121P GLY* 3.8 12.1 - - - -
122P PHE* 4.7 2.7 - - + -
138P PRO 4.3 2.2 - - - +
139P HIS* 3.2 13.9 - - + +
140P VAL* 3.7 33.4 - - + -
141P ASP* 3.8 4.7 - - - +
----------------------------------------------------------
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