Contacts of the strand formed by residues 124 - 133 (chain A) in PDB entry 5H4Y
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 GLN 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.5 6.2 - - - -
119A ASP 2.9 29.5 + - - -
122A SER* 3.3 29.6 + - - +
123A GLY* 1.3 82.5 - - - +
125A LEU* 1.3 59.2 + - - +
126A LEU* 3.7 13.0 + - + +
178A ALA* 3.6 22.6 - - + +
179A PHE 3.2 6.1 - - - +
180A LYS* 4.3 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.4 5.4 - - + -
117A ASP 4.1 9.6 - - - +
118A TYR* 3.9 13.2 - - + +
124A GLN* 1.3 70.3 - - - +
126A LEU* 1.3 69.6 + - - +
127A VAL* 3.7 20.8 + - + -
152A LEU* 4.2 25.6 - - + -
178A ALA* 3.1 4.2 - - - -
179A PHE* 2.8 40.2 + - + +
181A VAL* 4.2 9.2 - - + -
186A LEU* 4.2 6.3 - - + -
191A LEU* 5.2 0.7 - - + -
214A MET* 3.8 22.4 - - + -
219A LEU* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 3.6 1.4 + - - +
116A LEU* 3.4 5.9 - - - -
117A ASP* 2.7 64.4 + - + +
119A ASP* 4.2 16.4 - - + +
122A SER* 5.3 0.2 - - - +
124A GLN* 3.7 26.2 - - + +
125A LEU* 1.3 74.4 - - - +
127A VAL* 1.3 62.0 + - - +
128A GLY 4.0 0.4 + - - -
176A THR* 4.3 16.6 - - + -
177A PHE 3.5 4.7 - - - +
178A ALA* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER 3.5 7.0 - - - +
116A LEU* 4.1 2.7 - - + -
125A LEU* 3.9 20.2 - - + -
126A LEU* 1.3 75.4 - - - +
128A GLY* 1.3 61.6 + - - +
129A ILE* 3.9 23.7 + - + -
150A VAL* 4.1 10.8 - - + -
176A THR* 3.3 3.7 - - - -
177A PHE* 2.8 42.1 + - + +
179A PHE* 3.9 26.9 - - + -
191A LEU* 3.9 31.4 - - + -
193A MET* 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 3.1 11.8 - - - +
115A SER* 2.9 45.3 + - - -
126A LEU 4.0 1.0 - - - -
127A VAL* 1.3 71.8 - - - +
129A ILE* 1.3 62.9 + - - +
130A LEU* 3.6 7.4 - - - -
175A GLU 3.3 9.6 - - - -
176A THR* 4.0 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.1 10.5 - - + -
113A GLN 4.2 2.0 - - - -
114A TYR* 4.6 0.9 - - + -
127A VAL* 3.9 7.4 - - + +
128A GLY* 1.3 74.4 - - - +
130A LEU* 1.3 61.2 + - - +
148A VAL* 3.7 27.6 - - + -
150A VAL* 3.8 29.6 - - + -
162A THR* 4.1 13.9 - - + -
173A PHE* 3.3 20.3 - - + +
174A GLY 3.1 6.1 + - - -
175A GLU* 2.8 32.9 + - + +
177A PHE* 4.4 9.4 - - + -
193A MET* 3.6 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLN* 2.9 47.8 + - + +
114A TYR 4.5 2.7 - - - -
115A SER* 3.8 17.7 - - - +
128A GLY* 3.6 24.0 - - - +
129A ILE* 1.3 72.8 - - - +
131A GLN* 1.3 62.4 + - - +
172A HIS* 3.8 2.1 - - - +
173A PHE* 2.9 21.6 + - - -
174A GLY* 3.2 10.8 + - - +
175A GLU 5.2 0.7 - - - +
224A GLN* 3.6 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.4 6.1 - - - +
113A GLN* 2.8 54.3 + - + +
129A ILE 3.9 0.4 - - - -
130A LEU* 1.3 79.8 - - - +
132A ALA* 1.3 65.2 + - - +
133A MET* 5.4 3.6 - - - +
171A PRO 3.2 15.7 - - - +
172A HIS* 3.7 24.2 + - + -
173A PHE* 3.8 11.3 - - - -
226A TRP* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN 3.2 13.5 - - - +
112A LEU* 4.0 8.3 - - + +
131A GLN* 1.3 80.2 - - - +
133A MET* 1.3 63.7 + - - +
135A LEU* 3.8 21.8 - - + -
170A ASN* 3.2 23.9 - - - +
171A PRO* 3.0 27.3 + - + +
173A PHE* 4.0 9.1 - - + -
195A VAL* 5.6 1.3 - - + -
226A TRP* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLY* 3.3 1.2 - - - -
111A GLN* 2.8 45.7 + - + +
131A GLN* 5.4 3.4 - - - +
132A ALA* 1.3 77.0 - - - +
134A GLY* 1.3 67.5 + - - +
135A LEU* 3.2 4.0 + - - -
169A LEU 3.9 0.9 - - - -
170A ASN* 3.2 13.7 - - + +
226A TRP* 3.7 35.4 - - + -
----------------------------------------------------------
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