Contacts of the strand formed by residues 110 - 121 (chain A) in PDB entry 3BRW
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 GLY 110 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.2 5.6 - - - -
106A ASP* 2.8 37.3 + - - +
107A THR 4.8 0.6 - - - -
108A ALA 3.9 0.2 - - - -
109A LEU* 1.3 79.9 - - - +
111A HIS* 1.3 65.8 + - - -
112A LEU* 3.7 1.4 + - - +
134A LYS* 4.0 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER 4.2 4.3 - - - -
105A LEU* 4.0 13.6 - - + +
110A GLY* 1.3 74.2 - - - -
112A LEU* 1.3 67.6 + - - +
132A ARG 3.7 0.5 - - - +
134A LYS* 3.6 27.3 + - + +
391A ALA 4.9 1.8 - - - -
394A LEU* 3.4 28.3 - - + +
395A GLU* 3.5 48.2 - - + +
398A TYR* 3.4 42.7 - + + -
399A GLU* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.1 28.2 - - - +
104A SER 3.1 17.0 + - - +
106A ASP* 4.1 19.3 - - + +
109A LEU* 4.6 13.0 - - + -
110A GLY 4.0 10.1 - - - +
111A HIS* 1.3 84.1 - - - +
113A VAL* 1.3 64.0 + - - +
114A PHE* 4.1 0.7 - - + -
131A LEU* 3.9 19.1 - - + -
132A ARG 3.5 10.5 - - - +
133A THR* 3.9 12.6 - - - -
164A VAL* 4.2 18.6 - - + -
166A VAL* 4.2 8.7 - - + -
169A PHE* 4.1 29.3 - - + -
398A TYR* 4.2 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 6.0 2.0 - - + -
102A TYR 3.7 5.4 - - - +
103A TYR* 4.7 2.2 - - + +
111A HIS 4.3 0.2 - - - -
112A LEU* 1.3 76.6 - - - +
114A PHE* 1.3 60.5 + - - +
132A ARG* 2.9 63.8 + - + +
172A VAL* 6.0 0.7 - - + -
181A ILE* 4.5 9.0 - - + -
394A LEU* 3.8 24.5 - - + -
397A LEU* 4.2 15.0 - - + -
398A TYR* 4.5 18.2 - - + -
401A LEU* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE 4.1 0.2 - - - +
101A ASN* 3.7 1.5 - - - -
102A TYR* 2.8 43.5 + - + +
113A VAL* 1.3 75.9 - - - +
115A SER* 1.3 73.4 + - - +
116A LEU* 3.7 30.3 - - + -
129A LEU* 4.0 28.5 - - + -
130A LEU 3.3 16.4 - - - -
131A LEU* 3.6 31.9 - - + -
132A ARG* 4.2 0.2 - - - -
153A VAL* 3.9 25.8 - - + -
156A MET* 4.5 1.6 - - + -
157A ALA* 4.1 16.2 - - + -
160A VAL* 4.5 5.6 - - + -
169A PHE* 4.3 24.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.4 8.4 - - - -
94A PHE* 3.8 22.2 - - - -
100A PHE 3.3 7.2 - - - -
101A ASN* 2.9 21.2 + - - -
114A PHE* 1.3 93.5 - - - +
116A LEU* 1.3 63.0 + - - +
130A LEU* 2.7 26.5 + - - -
132A ARG* 2.4 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 3.6 4.9 - - - -
99A HIS* 3.3 3.1 - - - +
100A PHE* 2.9 65.0 + - + +
102A TYR* 3.7 19.7 - - + +
114A PHE* 3.7 28.7 - - + -
115A SER* 1.3 75.8 - - - +
117A LYS* 1.3 64.8 + - - +
118A TYR* 5.3 2.2 - - + +
127A LEU* 5.6 4.9 - - + -
128A ARG 3.5 5.6 - - - -
129A LEU* 3.7 17.0 - - + -
153A VAL* 4.1 0.9 - - + -
156A MET* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS* 2.9 46.8 + - + +
94A PHE* 3.6 18.8 - - + -
97A LYS* 4.3 23.0 - - - +
98A GLU 3.7 17.9 - - - +
99A HIS* 4.2 3.8 - - + +
100A PHE* 5.9 0.4 - - - -
116A LEU* 1.3 76.4 - - - +
118A TYR* 1.3 67.5 + - - +
119A ASP* 3.7 37.0 + - + +
127A LEU* 3.4 6.6 - - - +
128A ARG* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU 5.0 3.8 + - - +
100A PHE* 6.0 6.2 - - + -
116A LEU* 4.3 3.7 - - + +
117A LYS* 1.3 75.2 - - - +
119A ASP* 1.3 66.3 + - - +
120A VAL* 4.1 14.7 - - + +
125A GLU* 2.7 46.9 + - + -
126A HIS 4.1 9.2 - - - -
127A LEU* 4.1 12.8 - - + -
144A ILE* 4.7 4.0 - - + -
150A PHE* 3.4 37.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.7 35.7 + - + -
118A TYR* 1.3 79.3 - - - +
120A VAL* 1.3 82.5 + - - +
121A ILE* 4.9 3.5 - - - +
125A GLU* 3.7 1.6 - - - +
126A HIS* 2.8 60.5 + - + +
128A ARG* 5.2 1.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
118A TYR* 4.1 15.9 - - + +
119A ASP* 1.3 91.6 + - - +
121A ILE* 1.3 70.9 + - - +
122A GLY 3.4 27.4 + - - +
123A ASP* 3.8 10.8 - - - +
124A GLN 3.7 11.4 - - - +
125A GLU* 3.7 22.2 - - + +
126A HIS* 4.5 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
119A ASP* 4.9 4.3 - - - +
120A VAL* 1.3 77.4 - - - +
122A GLY* 1.3 60.9 + - - +
123A ASP 3.1 7.6 + - - -
124A GLN* 3.0 23.4 + - - +
126A HIS* 3.4 38.4 - - + +
249B GLN* 3.5 18.9 + - + +
87D GLN* 3.4 34.8 - - + +
125D VAL* 4.7 23.6 - - + +
----------------------------------------------------------
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