Contacts of the strand formed by residues 120 - 132 (chain S) in PDB entry 1H2I
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 TYR 120 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R PHE* 4.1 12.6 - + - -
84R TRP 4.9 0.4 + - - -
85R ALA* 2.9 52.3 - - + +
86R HIS 3.2 26.1 + - - -
87R SER* 3.9 15.6 + - - -
112R ARG* 4.9 6.2 + - - -
114R GLN* 3.1 30.8 + - - +
112S ARG* 3.6 42.8 - - + +
113S VAL 3.2 15.3 - - - +
114S GLN* 4.2 1.6 - - - -
118S GLY 3.1 17.7 - - - +
119S SER* 1.3 76.1 - - - +
121S HIS* 1.3 68.7 + - - +
158S PHE* 4.7 4.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R TYR 4.5 3.8 - - - -
84R TRP* 3.3 47.3 + + - -
86R HIS* 2.7 41.7 - + + -
112S ARG* 4.6 1.8 - - - -
113S VAL* 2.9 40.7 + - + +
120S TYR* 1.3 82.0 + - - +
122S GLU* 1.3 61.7 + - - +
154S ALA* 3.7 9.2 - - - +
157S SER* 3.4 31.6 - - - +
158S PHE* 3.6 34.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R HIS* 3.0 30.8 + - - +
87R SER* 3.4 21.4 - - - -
88R ILE* 2.8 48.7 + - + +
147R VAL* 4.5 0.9 - - - +
89S THR* 2.7 38.7 + - - +
110S PHE* 3.8 6.3 - - - +
111S VAL 3.2 19.7 - - - +
112S ARG* 4.0 12.0 - - + +
121S HIS* 1.3 77.0 - - - +
123S ASP* 1.3 66.0 + - - +
154S ALA* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R HIS* 5.0 3.9 + - + -
88R ILE* 3.7 11.2 - - - -
147R VAL* 3.5 18.2 - - - +
148R THR* 5.0 2.9 + - - -
151R LEU* 6.1 0.3 - - - +
110S PHE* 3.5 2.4 - - - -
111S VAL* 3.0 33.9 + - - +
122S GLU* 1.3 77.6 - - - +
124S VAL* 1.3 71.1 + - - +
150S GLY* 4.4 2.2 - - - +
153S ARG* 2.4 52.1 + - + +
154S ALA* 3.7 23.9 - - - +
157S SER* 5.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R ILE* 4.2 0.2 - - - +
91R GLN* 3.7 6.7 - - - +
143R ARG* 3.9 20.6 - - + +
144R LYS* 4.2 5.0 - - + -
147R VAL* 3.1 32.3 - - + -
108S CYS* 4.5 7.9 - - + -
109S ALA 3.2 8.1 - - - +
110S PHE* 3.1 38.8 - - + -
123S ASP* 1.3 86.7 + - - +
125S GLY* 1.3 64.6 + - - +
126S TYR* 6.4 0.2 - - + -
150S GLY* 4.0 2.5 - - - -
153S ARG* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144R LYS* 4.5 2.0 - - - -
108S CYS* 3.3 7.3 - - - +
109S ALA 2.8 29.4 + - - -
124S VAL* 1.3 77.3 - - - +
126S TYR* 1.3 62.0 + - - +
146S ALA 3.4 7.6 - - - -
149S ASP* 3.3 7.0 - - - -
150S GLY* 3.3 27.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R ALA* 3.7 15.0 - - - -
139R LEU* 3.5 16.4 - - + +
140R GLU* 3.6 45.9 - - + +
143R ARG* 3.8 13.5 - - + -
144R LYS* 4.1 4.2 - - + +
94S ASP* 2.6 33.5 + - - +
95S PHE* 4.0 2.3 - - - -
106S GLY* 3.3 31.2 - - - -
107S VAL 3.2 16.2 - - - -
108S CYS* 3.6 16.2 - - + -
124S VAL* 6.1 0.2 - - + -
125S GLY* 1.3 73.7 - - - -
127S GLY* 1.3 72.6 + - - +
128S VAL* 3.7 13.0 - - + -
145S GLU* 3.7 3.3 - - - +
146S ALA* 3.5 8.9 - - - -
149S ASP* 2.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106S GLY* 3.5 3.1 - - - -
107S VAL 2.7 35.9 + - - -
126S TYR* 1.3 74.7 - - - +
128S VAL* 1.3 65.1 + - - +
142S ALA* 3.3 29.4 - - - +
145S GLU* 4.2 6.3 - - - -
146S ALA* 3.6 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R ALA* 3.6 32.3 - - + -
137R LEU* 4.8 7.9 - - + -
140R GLU* 4.9 10.3 - - - +
105S VAL 3.4 3.1 - - - +
126S TYR* 3.7 20.2 - - + -
127S GLY* 1.3 80.2 - - - +
129S SER* 1.3 62.5 + - - +
130S GLU* 3.8 22.4 - - + +
141S LYS* 2.6 36.0 + - - +
142S ALA* 4.1 3.7 - - - +
145S GLU* 3.7 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103S PHE 3.3 6.3 - - - +
105S VAL* 2.8 36.8 + - - +
128S VAL* 1.3 79.0 - - - +
130S GLU* 1.3 62.4 + - - +
132S LEU* 3.7 14.9 - - - +
138S SER* 3.3 48.0 + - - -
141S LYS* 4.0 15.5 - - - +
142S ALA* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R SER* 2.8 30.3 + - - -
135R LYS 4.9 0.5 + - - -
136R ALA* 3.9 8.6 + - + +
137R LEU* 4.0 10.6 - - - +
95S PHE* 5.8 0.2 - - - -
103S PHE 3.6 2.5 - - - -
104S TYR* 3.6 29.4 - - + +
105S VAL 4.9 0.2 - - - +
128S VAL* 3.8 18.7 - - + +
129S SER* 1.3 81.0 + - - +
131S GLY* 1.3 59.9 + - - +
132S LEU* 3.6 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S LYS* 3.3 38.1 - - - +
103S PHE 3.0 9.9 + - - -
104S TYR* 3.7 10.6 - - - -
130S GLU* 1.3 73.9 - - - +
132S LEU* 1.3 68.5 + - - +
133S LYS* 3.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S LYS* 3.2 1.9 - - - -
103S PHE* 2.8 29.5 + - - -
129S SER* 3.7 19.3 - - - +
130S GLU 3.6 4.6 - - - +
131S GLY* 1.3 79.0 - - - +
133S LYS* 1.3 63.0 + - - +
134S SER* 4.0 7.0 - - - +
137S LEU* 4.1 27.8 - - + +
138S SER* 3.4 16.6 + - - +
141S LYS* 5.1 8.1 - - + -
----------------------------------------------------------
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