Contacts of the strand formed by residues 83 - 88 (chain A) in PDB entry 4XTB
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 LEU 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.2 4.6 - - - -
80A GLN 2.8 32.3 + - - +
81A ASN* 4.2 8.3 - - + +
82A GLY* 1.3 79.5 - - - +
84A PRO* 1.3 68.2 - - + +
85A VAL* 3.5 3.0 + - - +
100A THR* 4.0 23.1 - - + -
101A LEU 3.8 16.8 - - - +
102A LYS* 4.5 13.0 - - + -
103A PRO* 3.8 15.0 - - + -
173A ALA* 3.9 20.0 - - + -
174A ALA* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.2 9.0 - - + -
78A VAL 3.9 4.7 - - - +
79A TYR* 3.6 19.5 - - + -
83A LEU* 1.3 83.5 - - - +
85A VAL* 1.3 60.4 + - - +
86A ILE* 4.0 4.5 - - + -
99A PHE 3.7 0.9 - - - +
100A THR* 3.5 3.1 - - - +
101A LEU* 3.1 55.0 + - + +
103A PRO* 3.3 22.7 - - + -
141A ILE* 4.4 0.2 - - + -
145A LEU* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 3.6 1.9 + - - +
77A VAL* 3.4 2.8 - - - -
78A VAL* 2.8 40.8 + - + +
80A GLN* 4.0 32.5 - - + +
83A LEU 3.9 8.3 - - - +
84A PRO* 1.3 75.6 - - - +
86A ILE* 1.3 62.8 + - - +
87A SER* 3.9 3.0 + - - +
98A GLN* 3.6 43.7 - - + +
99A PHE 3.5 3.8 - - - +
100A THR* 3.6 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.7 22.0 - - + -
76A THR 3.2 10.5 - - - +
77A VAL* 4.0 23.3 - - + -
84A PRO* 4.9 2.9 - - + -
85A VAL* 1.3 76.2 - - - +
87A SER* 1.3 59.3 + - - +
88A VAL* 3.9 2.7 - - + -
98A GLN* 3.3 2.2 - - - -
99A PHE* 2.8 51.6 + - - +
101A LEU* 3.6 27.1 - - + -
111A PHE* 3.9 33.2 - - + -
144A LEU* 5.5 2.2 - - + -
145A LEU* 4.7 15.0 - - + -
149A PHE* 4.8 7.0 - - + -
160A VAL* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.3 6.6 - - - +
76A THR* 2.9 31.2 + - - -
85A VAL* 3.9 3.5 + - - -
86A ILE* 1.3 71.0 - - - +
88A VAL* 1.3 60.9 + - - +
96A ARG* 2.7 54.5 + - - +
97A CYS 3.5 6.8 + - - -
98A GLN* 4.2 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 4.3 16.8 - - + -
86A ILE* 3.9 25.6 - - + +
87A SER* 1.3 80.2 + - - +
89A ARG* 1.3 77.6 + - - +
90A LEU* 3.7 14.6 + - + +
96A ARG* 3.5 5.7 - - - -
97A CYS* 2.9 34.1 + - - +
99A PHE* 4.1 16.6 - - + -
111A PHE* 4.4 4.5 - - + -
115A LEU* 4.2 9.6 - - + -
151A LEU* 4.6 1.8 - - + -
153A ILE* 3.6 23.8 - - + -
----------------------------------------------------------
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