Contacts of the strand formed by residues 137 - 147 (chain H) in PDB entry 3IU3
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 THR 137 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H THR* 3.5 1.2 - - - -
134H SER* 2.8 41.8 + - - -
136H GLY* 1.3 79.5 - - - +
138H ALA* 1.3 60.8 + - - +
185H THR* 4.6 16.5 - - - +
186H VAL 3.1 15.9 - - - +
187H PRO* 4.9 3.6 - - + -
188H SER* 3.7 3.1 + - - -
111L SER* 5.5 1.4 + - - -
113L PHE* 4.4 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H PRO* 5.4 2.5 - - + -
132H SER 3.5 5.8 - - - +
133H THR* 3.8 20.2 - - + +
137H THR* 1.3 74.2 - - - +
139H ALA* 1.3 62.1 + - - +
140H LEU* 6.1 0.4 - - + -
184H VAL 3.8 1.0 - - - +
185H THR* 3.3 6.4 - - - -
186H VAL* 2.6 42.1 + - + +
188H SER* 3.9 12.3 + - - +
191H LEU* 4.3 24.0 - - + -
113L PHE* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H PRO* 4.1 6.0 - - - +
132H SER* 2.8 19.4 + - - -
138H ALA* 1.3 75.3 - - - +
140H LEU* 1.3 61.4 + - - +
183H VAL* 4.7 0.7 - - + -
184H VAL 3.6 4.5 - - - +
185H THR* 4.1 8.7 - - + -
113L PHE* 3.7 41.9 - - + -
115L PHE* 3.2 25.9 - - + -
132L LEU* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LEU 3.7 9.2 - - - +
128H PRO* 3.7 29.4 - - + -
138H ALA 5.8 0.2 - - - -
139H ALA* 1.3 76.0 - - - +
141H GLY* 1.3 59.7 + - - +
156H TRP* 3.6 30.1 - - + -
183H VAL* 3.2 7.0 - - - +
184H VAL* 2.8 46.1 + - + +
186H VAL* 4.2 21.5 - - + -
191H LEU* 5.1 4.7 - - + -
196H TYR* 3.9 35.2 - - + -
213H VAL* 3.9 12.1 - - + +
115L PHE* 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H PRO 3.8 0.2 - - - -
126H LEU* 2.8 44.6 + - - +
140H LEU* 1.3 78.4 - - - +
142H CYS* 1.3 61.4 + - - -
156H TRP* 3.5 14.4 - - - -
182H SER 3.0 13.9 - - - -
183H VAL* 4.0 3.4 - - - -
213H VAL* 3.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H VAL* 4.1 14.4 - - + -
124H PHE 3.5 5.4 - - - -
125H PRO* 5.0 1.3 - - - -
126H LEU* 4.3 3.8 - - - +
141H GLY* 1.3 79.0 - - - -
143H LEU* 1.3 60.1 + - - +
144H VAL* 3.6 7.7 + - + +
154H VAL* 5.2 0.2 - - + -
156H TRP* 3.8 6.4 - - + -
181H SER* 3.3 5.7 - - - -
182H SER* 2.7 38.7 + - - +
198H CYS* 2.0 52.7 - - + -
200H VAL* 5.0 0.2 - - + -
211H LYS* 4.6 7.0 - - - -
213H VAL* 4.3 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H SER 3.4 6.1 - - - +
123H VAL* 3.4 0.8 - - - -
124H PHE* 2.7 52.3 + - + +
126H LEU* 4.1 16.4 - - + +
142H CYS* 1.3 70.2 - - - +
144H VAL* 1.3 61.4 + - - +
145H LYS* 3.5 10.9 + - + +
179H SER* 4.1 14.6 - - - +
180H LEU 4.0 5.6 - - - +
181H SER* 3.4 18.2 - - - +
118L SER* 5.9 0.2 - - - +
121L GLN* 4.1 16.8 - - - +
128L SER* 3.7 29.6 - - - +
130L VAL* 4.5 14.6 - - + -
175L THR* 5.0 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H PRO* 3.5 28.5 - - + -
122H SER 3.8 2.9 - - - -
123H VAL* 4.4 4.3 - - + +
142H CYS* 4.4 10.8 - - + +
143H LEU* 1.3 70.3 - - - +
145H LYS* 1.3 59.0 + - - +
147H TYR* 3.9 14.0 - - + -
152H VAL* 4.1 8.1 - - + -
154H VAL* 4.4 8.5 - - + -
179H SER* 3.2 4.3 + - - -
180H LEU* 2.9 55.0 + - + +
182H SER 5.3 0.4 - - - +
200H VAL* 3.8 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H PRO* 3.5 1.2 - - - +
122H SER* 2.8 42.3 + - - +
124H PHE* 4.4 16.2 - - + -
143H LEU* 3.5 11.7 + - + +
144H VAL* 1.3 75.0 - - - +
146H ASP* 1.3 89.1 + - - +
147H TYR* 3.8 2.5 - - - -
173H GLN* 3.3 18.5 + - - +
178H TYR 4.0 0.2 - - - -
179H SER* 3.3 15.8 + - - +
121L GLN* 3.9 18.4 - - - +
126L THR* 4.7 11.0 - - - +
128L SER* 3.2 22.4 + - - +
175L THR* 5.2 2.8 - - - +
177L THR* 3.6 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H LYS* 2.7 36.4 + - - +
120H GLY 3.6 3.3 - - - +
122H SER* 5.3 2.6 - - - +
145H LYS* 1.3 97.8 - - - +
147H TYR* 1.3 56.9 + - - +
173H GLN* 3.0 26.3 + - - +
175H SER* 4.6 0.7 + - - -
177H LEU* 3.7 24.1 - - + +
178H TYR 3.0 13.7 + - - -
179H SER* 4.2 0.2 - - - -
126L THR* 5.4 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H LYS* 3.6 8.5 - - - +
121H PRO* 3.7 27.1 - - + -
144H VAL* 3.9 36.6 - - + -
145H LYS 4.4 0.2 - - - -
146H ASP* 1.3 78.3 - - - +
148H PHE* 1.3 62.4 + - - +
149H PRO 3.3 20.9 - - - -
150H GLU* 4.4 9.7 + - + -
152H VAL* 3.9 20.8 + - + +
170H ALA* 3.3 25.3 - - - +
177H LEU* 3.7 4.5 - - - +
178H TYR* 2.8 73.3 + - + -
179H SER* 3.9 2.2 - - - -
180H LEU* 3.4 16.4 - - + +
202H HIS* 3.9 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