Contacts of the strand formed by residues 129 - 142 (chain C) in PDB entry 2Z9I
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 129 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER* 3.9 8.3 - - - -
140B ARG* 3.1 8.5 + - - +
159B GLN* 3.0 28.9 + - - +
204B LEU* 4.1 3.6 - - + -
119C ALA 3.5 1.9 - - - +
120C ILE* 3.2 6.2 - - - -
121C GLY 2.9 26.9 + - - -
123C PRO* 3.6 28.9 - - + +
126C LEU* 3.0 18.5 + - - +
128C GLY* 1.3 75.7 - - - +
130C VAL* 1.3 61.5 + - - +
131C THR* 3.9 23.7 + - + -
168C ASN* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.7 20.6 - - + -
114B GLY* 5.3 0.2 - - - -
134B ILE* 3.4 20.3 - - + +
136B SER* 2.7 41.6 + - - +
8C VAL* 5.2 0.4 - - + -
12C ALA* 4.2 9.2 - - + -
16C VAL* 3.6 31.4 - - + -
118C LEU* 4.0 28.5 - - + -
119C ALA 3.4 7.4 - - - +
120C ILE* 4.3 8.1 - - + -
128C GLY 4.0 2.0 - - - +
129C THR* 1.3 76.7 - - - +
131C THR* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 4.1 3.6 - - - -
136B SER* 4.0 0.9 - - - +
161B ASP* 3.4 26.9 - - + +
203B GLY 4.5 3.6 - - - +
204B LEU* 5.2 2.0 - - + -
118C LEU* 3.3 6.8 - - - +
119C ALA* 2.9 45.5 + - - +
129C THR* 3.9 19.2 + - + -
130C VAL* 1.3 78.3 - - - +
132C THR* 1.3 60.4 + - - +
162C ALA* 3.9 0.8 - - - +
163C ALA* 2.9 42.2 + - + +
168C ASN* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY* 4.4 6.5 - - - -
134B ILE* 3.7 37.7 - - + +
161B ASP* 3.0 20.4 + - - +
8C VAL* 5.3 5.4 - - - +
116C PRO* 6.1 0.3 - - - +
117C VAL 3.7 6.3 + - - -
118C LEU* 4.0 9.1 - - - +
131C THR* 1.3 73.9 - - - +
133C GLY* 1.3 62.3 + - - +
161C ASP 4.4 1.9 - - - +
162C ALA* 3.5 12.5 - - - -
163C ALA 4.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 5.3 4.7 - - - -
116C PRO* 3.6 3.8 - - - +
117C VAL* 3.0 30.3 + - - +
132C THR* 1.3 80.1 + - - +
134C ILE* 1.3 68.4 + - - +
161C ASP* 3.8 5.8 - - - -
162C ALA* 3.6 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.6 9.6 - - + -
130A VAL* 3.4 44.4 - - + +
131A THR* 4.4 2.2 - - - +
132A THR* 4.0 26.7 - - + +
114C GLY* 3.6 25.8 - - - +
115C GLN 3.2 10.5 - - - +
116C PRO* 4.5 3.8 - - + -
117C VAL* 3.7 6.3 - - - -
133C GLY* 1.3 78.0 - - - +
135C VAL* 1.3 74.6 + - - +
136C SER 3.3 1.0 + - - -
160C THR* 2.8 19.9 + - - -
161C ASP* 3.3 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 4.2 16.6 - - + -
112C ARG 3.5 24.0 - - - +
113C VAL* 3.6 5.9 - - - +
114C GLY 2.9 26.4 + - - +
115C GLN* 2.9 24.0 + - + +
117C VAL* 4.0 17.7 - - + +
134C ILE* 1.3 74.6 - - - +
136C SER* 1.3 62.1 + - - +
137C ALA 3.9 8.7 - - - +
138C LEU* 3.8 33.2 - - + -
158C ILE* 4.2 10.8 - - + -
159C GLN 3.6 6.5 - - - +
160C THR* 4.9 1.3 - - - -
173C LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY 3.5 6.6 - - - +
129A THR* 4.2 2.0 - - - -
130A VAL* 2.6 52.5 + - - +
131A THR* 4.1 1.0 - - - +
113C VAL* 4.0 6.9 - - - +
134C ILE* 3.3 1.5 + - - +
135C VAL* 1.3 72.4 - - - +
137C ALA* 1.3 58.7 + - - +
159C GLN* 2.7 39.3 + - - -
160C THR 3.8 0.6 - - - -
161C ASP* 3.3 29.1 + - - -
203C GLY 4.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU 5.1 0.4 - - - +
128A GLY 4.6 4.5 - - - +
113C VAL* 4.0 8.3 - - - -
135C VAL* 3.6 3.7 - - - +
136C SER* 1.3 79.2 - - - +
138C LEU* 1.3 67.7 - - - +
140C ARG* 3.3 34.8 - - + +
157C ALA 4.9 0.4 - - - -
158C ILE* 3.7 1.6 - - - -
159C GLN* 2.8 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C SER 5.1 1.6 - - - +
111C LEU* 3.5 57.2 - - + +
112C ARG* 4.0 10.1 - - - -
113C VAL* 4.0 15.1 - - + +
135C VAL* 3.8 15.7 - - + -
137C ALA* 1.3 78.2 - - - +
139C ASN* 1.3 81.8 + - - +
140C ARG* 3.4 3.9 + - - -
157C ALA 4.0 1.3 - - - -
158C ILE* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 1.3 84.6 - - - +
140C ARG* 1.3 62.8 + - - +
141C PRO* 3.4 10.2 - - - +
156C ASP* 3.2 41.2 + - - +
157C ALA 2.9 10.8 + - - -
158C ILE* 5.9 0.2 - - - +
209C PRO* 5.5 3.8 - - - +
212C GLN* 5.4 0.6 - - - +
272C ARG* 5.5 11.7 - - + +
286C SER* 4.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 5.0 0.4 + - - -
126A LEU* 3.3 23.0 + - + +
127A GLU* 2.9 42.8 + - - +
129A THR* 3.1 15.4 + - - +
137C ALA* 3.3 17.6 - - + +
138C LEU 3.4 4.2 - - - +
139C ASN* 1.3 75.3 - - - +
141C PRO* 1.4 73.4 - - + +
142C VAL* 3.3 23.6 + - + +
155C LEU 3.0 3.2 - - - +
156C ASP* 4.4 0.4 - - - -
157C ALA 2.7 37.2 + - - +
159C GLN* 2.8 33.4 - - + +
206C PHE* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 5.9 0.9 - - - +
139C ASN 3.4 9.2 - - - +
140C ARG* 1.4 90.9 - - - +
142C VAL* 1.3 63.1 + - - +
143C SER 4.2 1.4 + - - -
154C VAL* 4.6 1.1 - - + -
155C LEU 3.2 7.9 - - - +
276C SER* 5.4 1.3 - - - +
278C ASP* 3.7 34.0 - - + +
279C ALA* 3.7 25.4 - - + +
282C ALA* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 5.8 0.9 - - + -
140C ARG* 3.5 19.5 - - + +
141C PRO* 1.3 78.8 - - - +
143C SER* 1.3 60.1 + - - +
144C THR* 3.4 11.7 - - + +
154C VAL* 3.2 5.0 - - - +
155C LEU* 2.7 52.0 + - + +
157C ALA* 4.2 1.6 - - + -
186C ALA* 4.8 2.7 - - + -
206C PHE* 3.7 45.8 - - + -
408F VAL* 3.7 28.5 - - + -
----------------------------------------------------------
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