Contacts of the strand formed by residues 118 - 126 (chain A) in PDB entry 6R4E
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 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 3.9 0.5 - - - +
112A SER* 2.8 48.7 + - - +
116A ASN 4.7 0.2 - - - -
117A GLU* 1.3 82.1 + - + +
119A ILE* 1.3 69.4 + - - +
153A ALA* 4.4 1.9 - - - +
156A VAL* 3.8 34.5 - - + -
157A LYS* 4.1 17.0 - - + -
160A TYR* 3.8 36.8 - + + -
170A PHE* 4.1 19.3 - + - -
173A LEU* 4.5 2.0 - - + -
189A PHE* 5.6 1.8 - + + -
190A LYS 3.5 4.0 - - - -
191A SER* 3.2 29.8 - - - -
193A HIS* 3.6 26.5 - + - -
194A PHE* 4.1 6.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY* 4.2 2.9 - - - -
57A ILE* 3.7 31.9 - - + -
59A LEU* 3.8 26.9 - - + -
91A ILE* 3.6 25.1 - - + +
109A PRO* 4.0 4.9 - - + -
110A GLN 3.1 13.2 - - - +
111A ARG* 4.0 14.4 - - + -
116A ASN* 4.4 7.0 - - + +
118A PHE* 1.3 81.0 - - - +
120A VAL* 1.3 63.8 + - - +
153A ALA* 5.1 0.7 - - - -
189A PHE* 3.6 5.0 - - - +
190A LYS* 3.0 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.7 1.1 - - - -
108A HIS* 4.5 0.7 - - - +
109A PRO* 3.4 2.7 - - - +
110A GLN* 3.0 29.5 + - + +
119A ILE* 1.3 77.8 - - - +
121A ILE* 1.3 75.3 + - - +
122A HIS 4.5 0.2 + - - -
149A THR* 4.3 16.1 - - + +
152A ILE* 4.2 6.1 - - + -
153A ALA* 3.9 33.4 - - + +
187A LEU* 3.9 17.5 - - + -
188A VAL 3.3 15.7 - - - +
189A PHE* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.6 27.8 - - + +
5A PHE 4.2 2.7 - - - +
91A ILE* 3.9 21.3 - - + +
92A ALA 3.2 23.3 - - - +
93A HIS* 3.5 28.0 - - + -
108A HIS* 4.0 3.1 - - + -
109A PRO* 3.8 28.0 - - + -
120A VAL* 1.3 79.9 - - - +
122A HIS* 1.3 60.4 + - - +
186A ALA 3.6 1.0 - - - +
187A LEU* 3.4 7.4 - - - -
188A VAL* 3.2 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A CYS 4.4 0.5 + - - -
4A ILE* 4.2 0.2 - - - -
93A HIS* 2.7 25.8 + - - -
108A HIS* 3.2 14.6 + - + -
121A ILE* 1.3 77.2 - - - +
123A ASN* 1.3 93.6 + - - +
124A GLY 3.2 29.5 + - - -
125A ILE 3.6 3.4 - - - -
126A ILE* 3.9 13.5 - - + -
148A ASP* 3.8 13.0 - - - -
149A THR* 3.1 39.1 + - + +
152A ILE* 4.0 2.3 - - + +
184A ALA 3.5 0.4 + - - -
185A PHE* 3.3 18.2 - - + +
186A ALA 3.3 3.6 - - - -
187A LEU* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A CYS* 2.7 43.6 + - - +
3A GLY 3.4 2.1 + - - -
4A ILE* 3.4 23.2 - - + +
93A HIS* 3.1 13.9 + - - -
122A HIS* 1.3 77.7 - - - +
124A GLY* 1.3 58.5 + - - +
185A PHE* 3.2 3.3 - - - -
186A ALA* 3.0 31.6 + - + +
205A SER* 4.0 18.3 + - - +
261A SER* 3.4 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A CYS 5.5 0.4 - - - +
98A THR* 4.5 5.9 + - - +
122A HIS* 3.2 15.7 + - - -
123A ASN* 1.3 74.3 - - - +
125A ILE* 1.3 70.6 + - - +
148A ASP* 4.1 2.6 - - - +
184A ALA* 3.6 9.9 - - - -
205A SER* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 3.8 35.4 - - + +
99A HIS* 3.5 25.8 - - + +
122A HIS* 3.9 0.2 - - - -
124A GLY* 1.3 80.0 - - - +
126A ILE* 1.3 71.7 + - - +
127A THR* 3.6 11.9 + - + +
148A ASP* 3.3 4.0 - - - -
183A GLY* 3.6 1.2 - - - -
184A ALA* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A HIS* 3.9 7.4 - - + -
125A ILE* 1.3 77.4 - - - +
127A THR* 1.3 66.1 + - - +
128A ASN* 3.2 22.4 - - - +
129A TYR* 3.4 32.5 + - + +
132A LEU* 4.3 4.0 - - + -
148A ASP* 2.7 19.7 + - + +
151A THR* 4.7 2.0 - - - +
152A ILE* 3.7 30.7 - - + -
181A LEU* 3.8 24.2 - - + -
182A GLU 3.3 7.9 - - - +
185A PHE* 3.9 39.0 - - + -
----------------------------------------------------------
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