Contacts of the strand formed by residues 3 - 11 (chain C) in PDB entry 1XPM
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 ILE 3 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA 4.2 11.2 - - - +
2C ALA* 1.3 81.8 - - - +
4C GLY* 1.3 62.4 + - - +
122C LYS* 3.8 49.5 - - + +
125C LEU* 4.1 7.4 - - + -
126C ALA* 4.0 13.7 - - + +
162C ILE* 4.0 14.6 - - + -
163C ALA 3.3 16.6 - - - +
164C HIS* 3.6 35.0 - - + +
166C PRO* 3.9 4.0 - - - -
170C ALA* 3.8 0.5 - - - +
171C LEU* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 4 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 1.3 78.8 - - - +
5C ILE* 1.3 66.0 + - - -
6C ASP 3.3 0.2 + - - -
162C ILE* 3.2 10.6 - - - -
163C ALA 2.9 32.7 + - - +
166C PRO* 3.5 4.9 - - - +
169C LEU 3.1 12.6 - - - -
171C LEU* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLY* 1.3 69.4 - - - -
6C ASP* 1.3 58.5 + - - +
7C LYS 3.5 24.0 - - - +
8C ILE* 4.0 19.3 - - + -
118C ILE* 4.7 12.8 - - + -
160C MET* 4.0 21.1 - - + -
161C VAL 3.7 4.5 - - - +
162C ILE* 3.9 16.6 - - + -
166C PRO* 3.4 3.0 - - - +
168C ILE* 3.2 15.3 + - + +
169C LEU* 2.8 45.8 + - + +
171C LEU* 4.8 9.4 - - + +
282C TYR* 5.1 0.4 - - + -
285C LEU* 3.8 28.9 - - + -
289C LEU* 6.4 0.4 - - + -
314C TYR* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLY 3.3 1.6 + - - -
5C ILE* 1.3 72.8 - - - +
7C LYS* 1.3 81.3 + - + +
132C LYS* 3.7 22.0 + - - -
161C VAL* 2.8 18.2 + - + +
163C ALA* 4.2 17.5 - - + -
164C HIS 5.4 0.2 - - - -
165C ASN 3.8 4.3 - - - +
166C PRO* 3.6 9.1 - - + +
167C SER* 2.8 49.7 + - - +
168C ILE* 3.6 13.1 - - - +
325C HIS* 4.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.5 6.0 - - - +
6C ASP* 1.3 102.4 - - + +
8C ILE* 1.3 63.8 + - - +
62C ILE* 3.2 40.1 + - + +
64C THR* 3.7 16.6 + - - +
67C ASP* 2.7 31.2 + - - +
132C LYS* 4.6 4.4 - - - +
160C MET* 3.4 2.6 - - - -
161C VAL* 3.0 35.8 + - + -
168C ILE* 4.0 6.3 - - - -
325C HIS* 5.4 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.0 9.9 - - + -
7C LYS* 1.3 78.5 - - - +
9C ASN* 1.3 68.0 + - - +
62C ILE* 4.1 5.9 - - - +
158C VAL* 4.2 3.6 - - + -
159C ALA 3.3 13.2 - - - +
160C MET* 3.7 23.1 - - + -
168C ILE* 4.0 19.7 - - + +
282C TYR 3.9 10.5 - - - +
285C LEU* 4.4 18.6 - - + -
286C ILE* 3.5 34.1 - - + -
289C LEU* 4.6 12.8 - - + -
325C HIS 5.6 1.4 + - - +
326C LEU* 4.8 6.4 - - + -
327C ASP* 4.6 6.2 + - - +
331C HIS* 4.2 10.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 1.3 78.5 - - - +
10C PHE* 1.3 77.6 + - - +
57C ASN 4.2 1.4 + - - -
58C ALA* 2.9 31.0 + - - +
61C ASP* 4.0 24.9 + - - +
62C ILE* 3.8 17.3 - - + -
158C VAL* 3.3 5.7 - - - +
159C ALA 2.8 30.6 + - - -
286C ILE* 3.8 5.6 - - - -
327C ASP* 5.3 3.5 - - - +
330C ALA* 5.7 1.0 - - - +
331C HIS* 2.7 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN* 1.3 92.0 + - - +
11C TYR* 1.3 63.7 + - - +
12C VAL* 3.9 23.8 - - + -
58C ALA* 4.2 4.3 - - - -
157C ALA 3.1 13.0 - - - +
158C VAL* 3.9 14.4 - - + -
269C TYR* 4.1 13.5 - + - -
273C VAL* 4.9 2.0 - - + -
276C ILE* 5.9 1.8 - - + -
283C LEU* 3.7 27.8 - - + -
286C ILE* 3.7 18.2 - - + -
331C HIS* 3.7 35.2 - + + -
334C LEU* 3.4 33.0 - - + +
335C LEU* 4.1 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 1.3 76.8 - - - +
12C VAL* 1.3 89.9 + - - +
13C PRO* 4.1 6.9 - - + +
14C LYS* 4.5 7.4 + - - +
49C GLN* 3.6 28.0 + - - +
54C MET* 3.9 27.1 - - + +
57C ASN* 3.7 27.6 - - + +
58C ALA* 3.9 20.4 - - + +
156C GLY* 3.2 3.6 - - - -
157C ALA 2.9 30.9 + - - +
334C LEU* 3.9 20.0 - - + -
371C ILE* 3.5 28.9 - - + +
----------------------------------------------------------
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