Contacts of the strand formed by residues 94 - 109 (chain A) in PDB entry 3UR9
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 LEU 94 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 3.7 41.5 - - + +
87A ILE 3.7 2.7 - - - -
88A LYS* 3.9 15.9 - - + -
92A GLY 3.8 11.0 - - - +
93A GLU* 1.3 82.7 - - - +
95A LEU* 1.3 58.9 + - - +
96A PRO* 3.5 9.7 - - + +
3B PRO* 3.5 48.5 - - + +
4B THR* 4.1 4.9 - - - +
7B SER* 3.7 12.8 + - - +
67B ASP* 4.9 1.0 + - - -
201B CL 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 4.0 0.2 - - - -
85A VAL 3.6 0.2 - - - +
87A ILE* 2.8 39.5 + - + +
89A ARG* 3.6 40.8 - - + +
93A GLU* 4.4 19.7 - - + +
94A LEU* 1.3 75.0 - - - +
96A PRO* 1.3 67.3 - - + +
97A LEU* 3.3 28.1 + - + +
133A GLY 4.4 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 6.3 3.4 - - - -
1A ALA* 6.1 1.6 - - + -
6A TRP* 3.8 24.9 - - + -
84A SER* 3.7 15.5 - - - +
85A VAL 3.3 10.3 - - - +
86A LEU* 4.6 1.8 - - + -
94A LEU* 3.5 11.2 - - + +
95A LEU* 1.3 90.8 - - + +
97A LEU* 1.3 64.8 + - - +
98A ALA 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A CYS 3.7 0.2 - - - +
84A SER* 3.3 5.0 - - - -
85A VAL* 2.8 42.3 + - + +
87A ILE* 3.4 25.4 - - + -
95A LEU* 3.6 35.9 - - + +
96A PRO* 1.3 78.1 - - - +
98A ALA* 1.3 61.9 + - - +
99A VAL* 3.7 2.6 + - - +
121A LEU* 4.1 24.2 - - + -
133A GLY* 4.2 23.1 - - - +
134A THR* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.3 12.1 - - + -
83A CYS 3.5 7.6 - - - +
84A SER* 4.7 1.6 - - - +
96A PRO 4.1 1.4 + - - -
97A LEU* 1.3 72.9 - - - +
99A VAL* 1.3 63.5 + - - +
121A LEU* 3.7 2.8 - - - +
122A LEU* 2.9 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.2 5.9 - - - +
83A CYS* 2.8 40.5 + - + +
85A VAL* 3.6 28.9 - - + -
97A LEU 3.9 1.8 - - - +
98A ALA* 1.3 81.1 - - - +
100A ARG* 1.3 62.6 - - - +
101A MET* 3.5 14.1 + - - +
119A GLY* 3.6 17.0 - - - -
120A MET 3.4 11.9 - - - +
121A LEU* 3.5 22.7 - - + -
122A LEU* 4.5 0.7 - - - +
143A TYR* 4.7 0.2 - - + -
167A VAL* 3.5 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 3.5 29.1 + - - +
81A THR 3.7 2.5 - - - -
82A VAL* 3.6 17.0 - - + +
99A VAL* 1.3 69.7 - - - +
101A MET* 1.3 70.8 + - - +
119A GLY* 3.2 0.6 - - - -
120A MET* 2.9 47.1 + - + +
122A LEU* 4.1 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A CYS* 3.5 19.7 - - - -
78A PRO 4.6 2.2 - - - +
80A GLY* 2.8 28.8 + - - -
81A THR 2.8 22.9 + - - +
83A CYS* 3.8 11.2 - - - -
99A VAL* 3.7 26.7 - - - +
100A ARG* 1.3 76.8 - - - +
102A GLY* 1.3 58.9 + - - +
117A GLN* 3.7 36.3 - - + +
118A SER 3.5 18.2 - - - +
119A GLY* 4.2 0.2 - - - -
143A TYR* 3.8 19.1 - - + -
154A CYS* 6.0 0.4 - - - -
169A CYS* 3.8 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.3 17.1 - - - +
100A ARG 3.7 1.4 + - - -
101A MET* 1.3 73.2 - - - +
103A ALA* 1.3 61.9 + - - -
117A GLN* 2.8 27.4 + - - -
118A SER* 2.7 20.9 + - - -
119A GLY* 4.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.4 22.8 - - - +
102A GLY* 1.3 73.9 - - - -
104A ILE* 1.3 67.1 + - - +
105A ALA* 3.9 6.0 + - + +
107A MET* 5.5 1.6 - - - +
117A GLN* 3.5 3.2 - - - -
118A SER* 3.3 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.6 29.4 - - + +
76A GLY* 4.1 3.8 - - - -
77A CYS 4.1 10.5 - - - +
79A GLU* 4.5 3.7 + - + +
102A GLY 3.9 0.2 + - - -
103A ALA* 1.3 74.4 - - - +
105A ALA* 1.3 66.7 + - - +
115A HIS* 4.0 26.7 - - + +
116A GLY 3.2 11.4 - - - +
117A GLN* 3.5 32.5 - - + +
171A VAL* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 3.9 7.3 + - + +
104A ILE* 1.3 78.4 - - - +
106A SER* 1.3 63.4 + - - +
107A MET* 3.4 26.2 - - + +
115A HIS* 4.3 6.1 - - - -
116A GLY 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA* 1.3 73.2 - - - +
107A MET* 1.3 62.0 + - - +
113A LEU* 4.3 18.1 - - - +
114A VAL 3.5 5.2 - - - -
115A HIS* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 5.7 0.7 - - - +
105A ALA* 3.4 33.2 - - + +
106A SER* 1.3 77.9 - - - +
108A ARG* 1.3 59.2 + - - +
109A ILE* 3.9 15.9 - - + -
112A ARG 3.5 0.2 - - - +
113A LEU* 3.3 8.7 - - - +
114A VAL* 2.7 39.3 + - + +
116A GLY* 3.7 25.8 - - - +
117A GLN* 4.1 2.9 - - - +
118A SER* 4.9 9.2 - - - +
168A VAL* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 1.3 74.8 - - - +
109A ILE* 1.3 64.6 + - - +
110A GLN 4.1 0.9 + - - -
111A GLY* 3.9 31.9 - - - +
112A ARG 3.4 4.5 - - - +
113A LEU* 4.7 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 4.3 14.4 - - + -
108A ARG* 1.3 79.5 - - - +
110A GLN* 1.3 72.0 + - + +
111A GLY 3.2 0.2 - - - -
112A ARG* 2.9 25.6 + - - +
114A VAL* 4.0 25.1 - - + -
159A ALA* 3.9 26.7 - - + -
168A VAL* 4.1 24.9 - - + -
203A K36 4.0 36.6 - - + +
----------------------------------------------------------
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