Contacts of the strand formed by residues 129 - 136 (chain O) in PDB entry 2AXT
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 PHE 129 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C GLY 4.4 5.6 - - - -
330C SER* 3.2 22.9 - - - -
331C ALA 3.7 16.8 - - - -
332C GLN* 3.7 24.0 - - + -
336C GLY 3.5 22.7 - - - -
337C LEU 4.1 4.3 - - - -
338C GLY* 3.8 10.8 - - - -
341C LEU 5.5 2.7 - - - -
104O LEU* 3.9 3.3 - - - +
127O ILE* 3.4 8.6 + - + +
128O ASP* 1.3 84.4 - - - +
130O GLN* 1.3 80.3 + - - +
131O PRO* 4.4 2.5 - - + -
145O LEU* 3.8 19.7 - - + -
146O PHE 3.4 9.9 - - - -
147O THR* 3.7 13.9 - - - +
149O LYS* 3.4 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU* 5.7 2.2 + - - +
342C MET* 5.2 5.3 - - - +
343C ARG* 3.6 24.8 + - - +
101O THR* 3.3 38.7 + - - +
102O THR* 3.7 14.6 - - - +
103O SER 3.5 20.4 - - - +
104O LEU* 4.0 3.6 - - + -
127O ILE* 3.5 24.1 - - + +
129O PHE* 1.3 83.0 - - - +
131O PRO* 1.3 77.0 - - - +
132O VAL* 3.2 4.1 + - + +
145O LEU* 4.4 3.3 - - - +
146O PHE* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 131 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.4 26.0 + - + +
335C THR 5.3 0.2 - - - +
336C GLY 3.0 29.6 - - - +
337C LEU* 3.2 30.7 - - + +
98O THR* 5.3 0.3 - - - +
101O THR 4.7 3.3 - - - +
129O PHE* 4.4 6.3 - - + +
130O GLN* 1.3 91.1 - - + +
132O VAL* 1.3 60.2 + - - +
144O LEU 3.7 7.4 - - - +
145O LEU* 4.2 4.5 - - + -
177O TYR* 3.6 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 5.8 0.2 - - - -
76O PHE* 3.9 26.0 - - + -
96O LEU* 3.9 21.3 - - + -
98O THR* 4.5 4.0 - - - +
101O THR 4.6 1.8 - - - +
102O THR* 3.8 28.0 - - + -
130O GLN* 3.2 11.6 + - + +
131O PRO* 1.3 76.9 - - - +
133O THR* 1.3 67.2 + - - +
134O VAL* 4.0 6.3 - - + -
143O PRO* 3.2 2.9 - - - +
144O LEU* 2.8 51.1 + - + +
146O PHE* 4.3 8.7 - - + -
177O TYR* 4.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 4.9 4.3 + - - +
107A TYR* 3.9 24.2 + - + +
96O LEU* 3.6 3.1 - - - +
97O VAL* 3.2 42.8 + - + +
98O THR* 3.5 13.5 + - - -
131O PRO 4.4 0.2 + - - -
132O VAL* 1.3 74.8 - - - +
134O VAL* 1.3 64.5 + - - +
141O ARG* 4.4 19.1 - - + -
142O ILE 3.6 5.2 - - - +
143O PRO* 3.3 25.1 - - + +
177O TYR* 3.6 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O PHE* 4.2 20.6 - - + -
78O VAL* 4.6 5.4 - - + -
94O THR* 3.4 30.3 - - + +
95O LYS 3.2 14.6 - - - +
96O LEU* 4.1 10.8 - - + -
132O VAL* 4.0 17.7 - - + -
133O THR* 1.3 80.0 - - - +
135O GLN* 1.3 59.4 + - - +
136O MET 3.6 0.9 + - - -
141O ARG* 4.4 1.6 - - - -
142O ILE* 2.7 55.4 + - + +
144O LEU* 4.8 4.5 - - + -
259O VAL* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 5.2 8.9 - - - +
103A ASP* 2.7 40.5 + - + +
106A LEU* 6.0 0.4 - - - +
489C UNK 5.4 5.9 - - - +
94O THR* 3.6 0.8 - - - -
95O LYS* 2.7 45.9 + - + +
97O VAL* 3.9 15.5 - - + +
134O VAL* 1.3 69.9 - - - +
136O MET* 1.3 66.6 + - - +
139O GLY* 3.5 12.2 + - - +
140O GLU 3.4 13.9 - - - +
141O ARG* 2.8 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 136 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O VAL* 4.1 28.0 - - + +
80O GLU* 5.8 8.3 - - + -
92O VAL* 6.1 5.6 - - + -
93O PRO 5.0 0.7 - - - +
94O THR* 3.5 24.9 - - + -
134O VAL 3.6 1.6 + - - -
135O GLN* 1.3 78.8 - - - +
137O ALA* 1.3 83.6 + - + +
138O GLY* 3.1 15.4 + - - +
139O GLY* 3.4 13.9 + - - +
140O GLU* 2.9 29.1 + - + +
142O ILE* 3.8 23.3 - - + -
257O HIS* 4.7 4.0 - - + -
5076b SER 4.7 0.3 - - - +
----------------------------------------------------------
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