Contacts of the strand formed by residues 162 - 170 (chain A) in PDB entry 3SKU
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 GLY 162 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.8 15.7 - - - -
160A THR 3.2 6.5 + - - -
161A ALA* 1.3 73.7 - - - +
163A THR* 1.3 63.1 + - - -
164A TYR* 3.6 6.6 - - - -
180A ILE* 3.9 5.9 - - - +
181A LEU 3.3 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.8 2.9 - - - +
102A MET* 2.9 47.1 + - + +
162A GLY* 1.3 72.2 - - - -
164A TYR* 1.3 78.2 + - - +
165A LEU* 5.0 0.4 - - + -
178A GLN* 4.0 22.9 - - + +
179A PHE 3.6 6.5 - - - +
180A ILE* 4.2 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.7 22.7 - - + -
99A TRP* 4.2 5.8 - + + -
100A PHE 3.6 5.4 - - - -
101A ARG* 3.7 18.8 - - - -
102A MET* 4.5 0.7 - - - -
110A ILE* 4.0 15.7 - - + -
138A TYR* 2.8 37.6 + + - -
151A PHE* 4.7 3.4 - + - -
153A MET* 3.6 24.7 - - + -
160A THR* 2.9 39.6 + - - +
162A GLY 3.6 13.9 - - - -
163A THR* 1.3 82.6 - - - +
165A LEU* 1.3 65.2 + - - +
178A GLN* 3.4 4.0 - - - -
179A PHE* 2.7 45.4 + - - +
181A LEU* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 4.2 23.8 - - + +
55A ILE* 5.9 0.9 - - + -
98A ALA 3.4 1.7 - - - +
99A TRP* 3.3 10.8 - - - -
100A PHE* 3.0 41.9 + - + +
102A MET* 4.0 32.5 - - + -
163A THR* 5.0 0.4 - - + -
164A TYR* 1.3 84.3 - - - +
166A ARG* 1.3 60.9 + - - +
176A ILE* 3.2 24.7 - - + -
177A THR 3.3 21.3 - - - +
178A GLN* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 4.7 0.4 + - - -
73A ALA* 3.3 31.3 + - - +
74A PRO 4.2 1.6 + - - -
75A SER* 3.3 18.9 - - - +
97A ILE* 4.8 3.4 - - + -
98A ALA 3.3 5.2 - - - +
99A TRP* 3.6 35.6 - - + +
100A PHE* 5.3 0.7 - - - -
149A LEU* 3.1 41.1 + - - +
165A LEU* 1.3 74.7 - - - +
167A LEU* 1.3 69.9 + - - +
168A VAL* 4.0 14.3 - - - +
175A GLU* 2.8 28.3 + - - -
176A ILE* 3.7 13.0 - - - +
177A THR* 2.8 47.4 + - - +
179A PHE* 4.1 9.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.5 39.0 - - + -
46A ASP 4.4 13.5 - - - +
47A PRO* 4.8 4.5 - - + -
96A THR 4.1 1.1 - - - +
97A ILE* 3.1 10.7 - - - +
98A ALA* 2.7 44.8 + - + +
100A PHE* 4.4 9.6 - - + -
166A ARG* 1.3 76.1 - - - +
168A VAL* 1.3 87.6 + - - +
169A LYS* 3.8 7.2 - - + +
174A THR* 3.4 32.1 - - + -
175A GLU 4.1 4.7 - - - +
176A ILE* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 4.1 3.4 - - - +
77A ALA* 3.5 28.0 - - + -
95A LEU* 3.7 19.5 - - + -
96A THR 3.5 2.5 - - - -
97A ILE* 4.2 10.3 - - + -
124A LEU* 5.1 0.4 - - + -
149A LEU* 3.9 24.7 - - + -
166A ARG* 4.0 18.4 - - - +
167A LEU* 1.3 81.9 - - - +
169A LYS* 1.3 60.6 + - - +
170A ILE* 4.2 1.6 - - + -
173A TRP* 3.8 9.0 - - + -
174A THR* 3.5 2.6 - - - -
175A GLU* 3.0 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 5.7 2.8 + - - -
45A PRO* 4.5 21.6 - - + +
49A GLN* 5.8 5.6 - - - +
94A ASN 3.3 4.3 - - - +
95A LEU* 4.2 0.2 - - - -
96A THR* 2.8 49.2 + - - +
167A LEU* 3.8 13.7 - - + -
168A VAL* 1.3 74.8 - - - +
170A ILE* 1.3 61.5 + - - +
171A ASN* 3.0 25.5 + - - +
172A ASP* 5.0 2.5 - - - +
173A TRP 3.0 17.9 - - - +
174A THR* 3.8 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 4.4 20.2 - - + +
80A ILE* 4.8 11.0 - - + -
81A VAL* 3.7 27.1 - - + -
93A TYR* 3.9 30.3 - - + -
94A ASN 3.4 2.7 - - - -
95A LEU* 3.4 24.0 - - + -
120A TYR* 5.7 1.3 - - + +
124A LEU* 3.8 18.4 - - + -
168A VAL* 4.2 1.3 - - + -
169A LYS* 1.3 70.5 - - - +
171A ASN* 1.3 60.2 + - + +
172A ASP 2.7 18.0 + - - -
173A TRP* 2.8 35.6 + - + +
----------------------------------------------------------
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