Contacts of the strand formed by residues 164 - 175 (chain C) in PDB entry 1D2H
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 VAL 164 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ASP 5.3 0.5 - - - +
129C GLY* 4.7 2.6 - - - -
130C PHE 3.4 7.6 - - - +
131C ASP 4.1 0.2 - - - +
133C VAL* 2.9 22.0 - - + -
160C ILE 3.9 0.4 - - - +
161C ALA* 3.3 25.2 + - - +
162C SER 4.5 3.5 - - - +
163C MET* 1.3 81.8 - - - +
165C ARG* 1.3 59.4 + - - +
166C PRO* 4.1 1.2 - - - +
168C GLY* 3.1 37.9 - - - -
169C LEU 3.2 19.1 - - - +
170C LEU* 4.6 3.1 - - + -
258C PHE* 3.9 18.4 - - + -
290C LYS* 3.0 26.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C HIS* 4.8 6.5 + - - +
56C GLY 4.6 7.9 + - - -
57C CYS* 4.6 7.1 - - - -
128C ASP 4.7 2.7 - - - +
129C GLY* 4.0 20.4 - - - +
130C PHE 2.9 11.5 + - - +
131C ASP* 2.4 50.1 + - - +
164C VAL* 1.3 74.8 - - - +
166C PRO* 1.3 96.9 + - + +
167C GLY* 3.1 22.6 + - - -
168C GLY* 2.6 19.6 + - - -
290C LYS* 3.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ASP 5.2 5.4 - - - +
164C VAL 4.2 2.2 - - - +
165C ARG* 1.3 110.3 + - + +
167C GLY* 1.3 54.1 + - - +
290C LYS* 3.5 21.3 - - + +
292C GLY* 3.3 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C HIS* 5.9 1.7 - - - +
57C CYS* 5.4 1.6 - - - -
131C ASP 4.7 0.2 - - - +
165C ARG* 3.1 19.6 + - - -
166C PRO* 1.3 74.9 - - - +
168C GLY* 1.3 56.2 + - - +
169C LEU* 4.8 1.0 - - - +
289C LYS* 2.8 40.2 + - - -
290C LYS 2.7 14.6 + - - -
291C THR* 4.8 2.3 - - - +
292C GLY 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C CYS* 5.7 0.2 - - - -
131C ASP 3.5 9.2 - - - -
164C VAL* 3.1 16.6 - - - -
165C ARG* 2.6 16.3 + - - -
167C GLY* 1.3 78.0 - - - +
169C LEU* 1.3 61.4 + - - +
288C LEU 3.4 1.1 - - - -
289C LYS* 2.8 35.5 - - - -
290C LYS* 3.0 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.3 34.3 - - + +
52C LEU* 4.4 7.9 - - + -
55C HIS* 3.6 31.9 - - + +
57C CYS* 4.0 11.4 - - - -
131C ASP 3.1 11.5 + - - +
132C ALA* 4.1 7.9 - - + -
133C VAL* 2.9 31.1 + - - +
164C VAL* 3.2 3.1 - - - +
167C GLY 4.8 0.9 - - - +
168C GLY* 1.3 93.6 - - - +
170C LEU* 1.3 62.3 + - - +
171C VAL* 5.3 3.4 - - + -
287C VAL* 4.5 7.6 - - + -
288C LEU 2.6 13.2 - - - +
289C LYS* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 2.9 23.6 - - + +
134C ILE* 5.1 0.2 - - - -
135C CYS* 5.0 2.9 - - + -
157C LEU* 6.1 0.4 - - + -
160C ILE* 3.3 32.5 - - + -
161C ALA* 5.2 1.8 - - + +
164C VAL* 4.6 2.2 - - + -
169C LEU* 1.3 77.8 - - - +
171C VAL* 1.3 62.6 + - - +
172C ILE* 4.1 25.8 - - + +
254C VAL* 4.2 10.8 - - + -
257C ALA* 5.9 0.9 - - + -
258C PHE* 3.7 33.9 - - + -
286C HIS 2.9 15.2 - - - +
287C VAL* 3.2 1.4 - - - -
288C LEU* 2.9 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C TRP* 3.6 30.5 - - + -
48C LEU* 4.8 7.0 - - + -
51C LEU* 5.3 8.3 - - + -
52C LEU* 5.4 3.4 - - + -
132C ALA* 6.3 0.2 - - + -
133C VAL 3.1 7.7 + - - -
134C ILE* 3.7 24.4 - - + +
135C CYS 3.0 18.5 + - - -
136C LEU* 3.0 36.3 - - + +
169C LEU* 5.3 3.4 - - + -
170C LEU* 1.3 77.0 - - - +
172C ILE* 1.3 58.5 + - - +
285C ILE* 3.7 13.9 - - + -
286C HIS 3.4 4.7 - - - +
287C VAL* 5.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C CYS* 2.7 38.4 - - + +
140C PHE* 4.5 10.8 - - + -
157C LEU* 4.0 22.7 - - + -
160C ILE* 4.5 12.3 - - + -
170C LEU* 3.6 27.7 - - + -
171C VAL* 1.3 76.4 - - - +
173C ASP* 1.3 66.2 + - - +
250C PHE* 3.3 36.1 - - + -
254C VAL* 4.9 2.5 - - + -
286C HIS* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C CYS 3.2 6.6 + - - +
136C LEU* 3.4 6.8 - - + -
137C GLY 2.9 14.3 + - - -
138C ASN* 2.8 28.8 + - - -
140C PHE* 4.5 10.7 - - - +
141C ALA 5.4 0.2 + - - -
171C VAL 3.8 0.2 + - - -
172C ILE* 1.3 81.4 - - - +
174C HIS* 1.3 71.0 + - - +
193C TYR* 2.7 29.1 + - - -
250C PHE* 5.1 0.2 - - - -
283C TYR* 4.4 7.8 - - + -
284C PHE 3.0 17.5 - - - +
285C ILE* 4.0 17.0 - - + +
286C HIS 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASN* 3.6 11.7 - - - +
140C PHE* 5.9 0.4 - - + -
141C ALA* 5.2 6.5 - - + +
173C ASP* 1.3 84.7 + - - +
175C LYS* 1.3 77.3 + - - +
177C TYR* 4.9 0.9 - - + -
245C HIS* 3.4 31.2 + - + +
247C LEU* 4.1 9.6 + - + -
250C PHE* 3.6 40.8 - - + -
283C TYR* 4.6 2.2 - - - -
284C PHE* 3.0 42.3 + + + +
286C HIS* 3.5 27.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASN* 3.0 24.4 + - - +
174C HIS* 1.3 87.5 - - - +
176C ASN* 1.3 52.9 + - - +
177C TYR* 2.6 45.2 + - + +
180C ILE* 4.4 16.8 - - + -
186C ALA* 5.9 5.2 - - + -
187C PRO 5.4 7.9 - - - -
190C LYS* 5.7 6.3 - - - -
191C ASN 6.2 0.7 - - - +
242C TYR* 5.8 1.8 - - - -
282C CYS* 3.5 17.9 - - + +
283C TYR* 2.8 43.5 + - + +
----------------------------------------------------------
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