Contacts of the strand formed by residues 151 - 159 (chain C) in PDB entry 1U1C
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 151 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C VAL* 3.3 21.4 - - + +
109C VAL* 3.8 27.4 - - + -
141C VAL* 5.4 4.7 - - + +
144C ALA* 3.4 25.6 + - + +
145C LYS* 5.9 7.5 - - - -
149C ALA 2.7 17.3 + - - -
150C THR* 1.3 74.0 - - - +
152C HIS* 1.3 76.1 + - - +
153C VAL* 5.0 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C HIS* 4.2 23.6 + - + -
102C ILE* 3.6 31.6 - - + +
106C ASP* 3.3 29.9 + - + -
107C VAL 3.1 5.9 + - - -
108C LEU* 3.4 24.0 - - + -
109C VAL 3.0 24.1 + - - -
150C THR* 4.2 11.4 - - + +
151C THR* 1.3 81.7 + - - +
153C VAL* 1.3 63.2 + - - +
193C MET* 3.6 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 4.2 22.7 - - + -
109C VAL* 3.4 20.2 - - + +
111C THR* 3.7 23.3 - - + -
137C THR* 4.7 1.1 - - + -
141C VAL* 3.9 29.4 - - + -
151C THR* 5.0 5.6 - - + +
152C HIS* 1.3 80.5 - - - +
154C GLY* 1.3 60.4 + - - +
193C MET* 3.8 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C VAL 3.2 7.1 + - - -
110C THR* 3.5 8.5 - - - +
111C THR* 2.9 37.7 + - - -
153C VAL* 1.3 76.5 - - - +
155C VAL* 1.3 61.6 + - - -
191C GLY 5.8 0.4 - - - -
193C MET* 3.5 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 4.2 19.5 - - + -
129A PRO* 3.8 11.9 - - + -
131A VAL* 3.9 28.3 - - + -
207A ALA* 5.0 7.0 - - + +
111C THR* 4.4 0.9 - - - +
112C ALA 3.4 12.6 - - - +
114C VAL* 3.7 28.5 - - + -
154C GLY* 1.3 75.5 - - - -
156C THR* 1.3 65.7 + - - +
191C GLY 4.9 4.4 + - - +
192C VAL* 3.6 12.8 - - + +
193C MET* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 5.7 0.3 - - - +
110C THR* 2.6 34.9 + - - +
112C ALA 3.2 4.8 + - - -
113C SER* 3.1 10.3 - - - -
114C VAL 2.7 30.0 + - - -
154C GLY 4.0 0.4 + - - -
155C VAL* 1.3 75.8 - - - +
157C ALA* 1.3 60.1 + - - +
192C VAL* 4.1 2.0 - - - -
193C MET* 4.1 2.4 - - - +
194C ASN* 2.7 40.5 + - - +
196C GLU* 3.6 28.7 - - + +
199C SER* 4.1 2.9 - - - +
215C MET* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C VAL* 3.9 13.7 - - + -
116C LEU* 4.2 11.7 - - + -
156C THR* 1.3 70.1 - - - +
158C SER* 1.3 59.3 + - - +
159C SER 3.8 1.1 + - - -
187C TRP* 4.5 7.0 - - + -
192C VAL* 3.5 16.0 - - + +
194C ASN 2.9 16.4 + - - +
195C TYR* 3.4 29.4 - - + -
196C GLU 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C SER* 4.2 2.0 - - - -
114C VAL 3.0 9.9 + - - -
116C LEU* 3.1 29.9 + - - +
117C ASP* 3.7 6.0 + - - +
156C THR 3.6 0.8 + - - -
157C ALA* 1.3 69.7 - - - +
159C SER* 1.3 58.9 + - - +
196C GLU* 2.7 25.6 + - - -
197C MET 3.7 1.7 - - - -
198C GLU 3.5 7.3 + - - -
199C SER* 3.3 13.1 + - - -
200C ALA* 3.1 33.9 + - - +
201C THR 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.6 13.7 - - - -
117C ASP* 5.0 1.3 - - - -
157C ALA 3.8 0.6 + - - -
158C SER* 1.3 74.0 - - - +
160C ASP* 1.3 59.3 + - - +
161C THR 2.7 31.3 + - - -
165C GLY* 3.6 18.2 - - - -
166C GLN* 4.1 10.1 - - - -
195C TYR* 4.8 2.9 - - - -
196C GLU 2.9 10.0 + - - -
197C MET* 3.2 32.9 - - - +
122D HIS* 3.2 15.3 + - - -
----------------------------------------------------------
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