Contacts of the strand formed by residues 139 - 148 (chain A) in PDB entry 2HXB
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 LYS 139 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.7 13.2 - - + +
104A ILE 3.3 5.4 - - - -
105A GLU* 3.8 35.4 + - + +
106A LEU 6.0 1.1 - - - -
137A GLY 3.6 10.9 + - - +
138A PHE* 1.3 94.9 - - - +
140A GLY* 1.3 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.6 22.1 - - - -
104A ILE* 2.9 36.6 + - - +
138A PHE* 3.4 6.6 - - - -
139A LYS* 1.3 74.8 - - - +
141A LYS* 1.3 66.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 3.4 22.1 - - + +
100A THR* 3.6 12.6 + - - +
101A ASN* 3.4 22.2 + - - +
102A GLU 3.4 17.3 - - - +
103A TYR* 4.0 17.2 - - + -
138A PHE* 3.7 11.6 - - - -
140A GLY* 1.3 77.3 - - - -
142A ILE* 1.3 63.0 + - - +
143A THR* 3.9 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.9 3.1 - - + -
99A THR* 3.2 6.1 - - - -
100A THR* 3.0 49.9 + - + +
102A GLU 4.8 0.7 - - - +
104A ILE* 4.4 21.3 - - + -
114A TYR* 4.3 28.3 - - + -
128A HIS* 4.8 4.3 - - - +
134A ILE* 4.4 17.5 - - + -
138A PHE* 4.7 5.6 - - + -
141A LYS* 1.3 76.7 - - - +
143A THR* 1.3 74.2 - - - +
144A LEU* 3.6 3.3 + - + -
164A LEU* 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.3 22.9 - - + -
98A GLY 3.5 12.2 + - - +
99A THR* 4.5 1.8 + - - +
128A HIS* 3.6 17.2 + - - -
141A LYS 3.9 3.0 + - - -
142A ILE* 1.3 85.2 - - - +
144A LEU* 1.3 68.5 + - - +
145A GLU* 4.2 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.8 23.6 - - + -
96A VAL 3.8 0.2 - - - +
97A LEU* 3.2 10.2 - - - +
98A GLY 2.8 33.6 + - - +
99A THR 3.7 31.2 - - - +
100A THR* 4.1 10.1 - - + +
114A TYR* 3.6 38.4 - - + +
127A SER* 3.4 8.5 - - - +
142A ILE* 4.3 2.5 - - + +
143A THR* 1.3 80.8 - - - +
145A GLU* 1.3 62.5 + - - +
146A ILE* 3.7 13.2 - - + -
161A ILE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL 4.0 2.2 - - - -
97A LEU* 3.7 20.6 - - + -
126A THR 3.4 0.5 - - - +
127A SER* 2.9 20.7 + - - -
128A HIS* 3.6 27.1 + - - -
129A GLN* 2.8 60.4 + - + +
130A THR* 4.1 6.0 + - - +
143A THR* 4.4 10.6 - - + +
144A LEU* 1.3 73.2 - - - +
146A ILE* 1.3 59.3 + - - +
147A VAL* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.1 12.8 - - + -
40A PHE* 3.8 32.1 - - + -
67A VAL* 4.1 8.5 - - + -
94A GLY 3.6 2.1 - - - +
95A GLY* 3.6 0.9 - - - -
96A VAL* 2.8 55.4 + - + +
98A GLY 4.5 2.0 - - - +
125A LEU* 4.0 20.6 - - + -
126A THR 3.0 8.3 - - - +
127A SER* 4.0 11.7 - - - -
144A LEU* 4.0 24.5 - - + -
145A GLU* 1.3 73.0 - - - +
147A VAL* 1.3 67.9 - - - +
155A LEU* 4.2 17.7 - - + -
161A ILE* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.8 0.2 - - - -
69A PRO* 5.8 0.2 - - + -
70A LEU* 5.6 5.2 - - + +
94A GLY* 4.3 13.2 - - - +
95A GLY* 4.2 13.7 - - - -
124A PHE 3.8 1.2 - - - +
125A LEU* 3.8 4.4 - - - -
126A THR* 2.9 40.7 + - - +
129A GLN* 3.8 23.1 - - + +
145A GLU* 3.7 2.5 + - + +
146A ILE* 1.3 82.2 - - - +
148A ALA* 1.3 69.5 + - - +
149A PHE* 3.4 30.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.8 31.0 - - + +
68A CYS 4.9 1.8 + - - -
69A PRO* 3.3 29.3 - - + +
70A LEU 4.4 0.5 + - - -
124A PHE 3.4 5.8 - - - +
125A LEU* 3.9 15.9 - - + -
147A VAL* 1.3 81.4 - - - +
149A PHE* 1.3 61.7 + - - +
150A ASP 3.7 0.4 - - - -
151A LYS 4.0 16.6 - - - +
153A VAL* 4.3 4.3 - - + -
----------------------------------------------------------
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