Contacts of the strand formed by residues 121 - 128 (chain H) in PDB entry 2I9B
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 121 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H CYS* 4.1 5.2 - - - -
115H CYS* 4.5 2.2 - - - -
118H PRO 5.3 0.4 - - - +
119H GLU 3.5 11.5 + - - +
120H GLU* 1.3 80.3 - - - +
122H CYS* 1.3 68.2 + - - +
123H LEU* 3.5 0.3 - - - +
147H CYS* 3.4 6.2 - - - -
148H GLY 3.0 33.7 + - - +
149H TYR* 5.3 5.5 - - + -
153H CYS* 3.4 29.3 - - - +
154H PRO* 4.0 20.9 - - - +
170H CYS* 4.2 3.1 - - - +
171H CYS 3.5 12.2 + - - +
172H GLN* 3.6 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLU 4.1 0.7 - - - -
95H CYS* 2.0 52.0 - - + -
121H GLN* 1.3 74.6 - - - +
123H LEU* 1.3 60.0 + - - +
146H GLY 3.6 1.8 - - - -
169H LYS 3.7 0.4 - - - +
170H CYS* 3.4 7.1 - - - +
171H CYS* 3.2 44.6 + - - +
172H GLN 4.4 4.3 - - - -
173H THR 3.8 8.7 - - - -
176H CYS* 3.4 24.2 - - + -
177H ASN* 3.9 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU* 4.1 11.7 - - + -
121H GLN 3.5 4.0 - - - +
122H CYS* 1.3 84.3 - - - +
124H ASP* 1.3 60.5 + - - +
125H VAL* 4.1 9.9 - - + -
144H LEU 4.4 0.9 - - - +
145H ARG* 3.4 2.7 - - - -
146H GLY 3.1 21.7 + - - +
147H CYS 3.5 18.8 - - - +
148H GLY* 3.4 34.1 - - - +
150H LEU* 3.8 28.5 - - + -
153H CYS* 3.6 25.8 - - - -
168H LEU* 4.9 1.3 - - + -
169H LYS 3.3 4.5 - - - +
170H CYS* 3.7 7.4 - - - -
177H ASN* 3.0 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H LEU* 1.3 75.9 - - - +
125H VAL* 1.3 64.1 + - - +
126H VAL* 3.6 21.4 + - - +
143H HIS* 5.1 4.0 + - - +
144H LEU 3.2 12.6 + - - +
145H ARG* 3.4 36.4 + - + +
167H PHE* 3.9 3.2 - - - +
168H LEU* 3.9 0.4 - - - +
169H LYS* 2.7 61.5 + - + +
177H ASN* 4.6 7.2 - - + +
182H LEU* 4.6 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASN* 5.9 0.9 - - - +
23D LYS* 3.8 4.0 - - + +
24D TYR* 3.5 28.0 - - + +
55H LEU* 4.5 13.0 - - + -
123H LEU* 4.8 5.6 - - + -
124H ASP* 1.3 76.3 - - - +
126H VAL* 1.3 63.3 + - - +
127H THR* 3.8 16.5 + - - +
140H ASP* 5.9 1.6 - - - +
141H ASP 4.8 1.6 - - - +
142H ARG 3.9 1.2 - - - +
143H HIS* 3.6 2.6 - - - -
144H LEU* 2.7 54.8 + - + +
150H LEU* 4.0 26.0 - - + -
167H PHE 3.7 3.8 - - - +
168H LEU* 4.4 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LYS* 4.4 1.4 - - - -
124H ASP* 4.1 17.3 - - - +
125H VAL* 1.3 75.4 - - - +
127H THR* 1.3 71.2 + - - +
142H ARG* 3.8 9.6 - - - +
143H HIS* 4.1 23.6 - - + +
165H PHE* 3.6 34.3 - - + +
166H HIS* 3.7 3.6 + - - -
167H PHE* 2.8 51.8 + - + +
182H LEU* 4.1 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LYS* 2.8 29.2 + - + -
125H VAL* 3.8 7.7 - - - +
126H VAL* 1.3 80.5 + - - +
128H HIS* 1.3 60.7 + - - +
130H ILE* 3.5 32.1 - - + +
140H ASP* 4.2 20.6 + - + +
141H ASP 4.2 10.0 + - - -
142H ARG* 3.0 34.6 + - - +
165H PHE 3.7 4.3 - - - -
166H HIS* 3.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLY* 5.5 10.6 + - - -
127H THR* 1.3 72.8 - - - +
129H TRP* 1.3 88.9 + + + +
130H ILE* 3.3 2.7 + - - +
142H ARG* 3.0 53.5 + - - +
163H ASP 4.2 6.1 + - - -
164H THR* 3.3 7.7 + - - -
165H PHE* 2.9 44.5 + - + +
166H HIS* 4.8 0.2 + - - -
----------------------------------------------------------
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