Contacts of the strand formed by residues 155 - 163 (chain A) in PDB entry 3G4C
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 TYR 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.4 15.9 - - - +
7A ASP* 2.7 23.8 + - - -
8A LYS* 3.2 19.4 + - + -
9A GLY* 3.6 24.9 - - - -
67A LYS* 3.8 23.8 - - + -
68A ALA* 3.4 22.0 - - - -
69A PRO* 3.7 16.4 - - + -
87A LEU* 4.7 6.6 - - - +
94A LEU* 5.9 1.6 - - - +
97A GLU* 2.9 30.2 + - + +
98A PHE 3.6 13.7 - - - -
99A TYR* 3.4 27.5 - - + +
153A ASN 3.5 0.6 + - - -
154A LEU* 1.3 85.0 - - - +
156A THR* 1.3 58.5 + - - +
186A TYR* 3.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 3.4 5.8 - - - +
68A ALA 2.8 39.9 + - - +
70A ILE* 4.1 19.7 - - + -
73A ALA* 3.9 22.7 - - + -
86A GLU* 2.6 38.2 + - + +
87A LEU* 3.8 15.5 + - - +
154A LEU* 3.6 1.0 + - - -
155A TYR* 1.3 75.2 - - - +
157A ARG* 1.3 67.7 + - - +
158A PHE* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.1 12.1 - - - -
65A HIS* 3.2 32.2 + - - +
66A VAL 3.2 4.9 - - - +
67A LYS* 3.8 24.2 - - + +
86A GLU* 3.3 3.1 - - - +
87A LEU* 3.0 54.6 + - + +
156A THR* 1.3 80.4 + - - +
158A PHE* 1.3 66.1 + - - +
28B ARG 5.4 1.4 + - - -
29B VAL* 2.7 36.7 + - + +
30B SER* 4.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE 3.9 0.3 - - - +
65A HIS* 3.4 3.6 - - - -
66A VAL* 2.9 70.0 + - + -
68A ALA* 4.6 7.4 - - + -
73A ALA* 4.2 17.5 - - + -
76A TRP* 3.8 28.5 - + - -
77A PHE* 3.6 37.9 - + + -
84A TYR* 4.1 4.5 - + - -
85A ASN 3.0 14.8 - - - +
86A GLU* 3.8 7.9 - - + -
156A THR* 4.7 4.7 - - + -
157A ARG* 1.3 81.5 - - - +
159A PHE* 1.3 77.0 + - - +
160A TRP* 4.0 16.4 - - + -
29B VAL* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.1 26.5 - - + -
63A THR* 3.9 16.6 - - + -
64A PHE 3.2 3.6 - - - -
65A HIS* 3.4 35.4 - + + -
84A TYR* 3.3 8.0 - - - -
85A ASN 2.8 32.7 + - - +
158A PHE* 1.3 76.5 - - - +
160A TRP* 1.3 59.5 + - - +
22B SER 5.2 0.7 - - - -
25B ARG* 3.6 26.2 - - + -
26B ALA* 3.8 22.2 - - + -
29B VAL* 4.0 9.4 - - + -
30B SER 3.9 35.2 - - - -
59B HIS* 4.0 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE 3.6 0.9 - - - +
63A THR* 3.2 2.7 - - - -
64A PHE* 2.7 68.3 + + + +
66A VAL* 4.8 0.4 - - + -
76A TRP* 3.4 42.4 - + - -
79A HIS* 5.1 3.8 - - + -
82A ALA* 3.3 13.6 - - + +
83A SER 3.4 10.1 - - - -
84A TYR* 3.2 38.6 + + - -
158A PHE* 4.0 12.3 - + + -
159A PHE* 1.3 74.2 - - - +
161A THR* 1.3 62.7 + - - +
162A VAL* 3.7 33.9 - - + -
166A SER* 5.5 0.4 - - - -
167A LEU* 5.1 2.0 - - + -
170A PHE* 3.8 33.0 - + + -
190A ILE* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 3.7 20.9 - - + -
62A PHE 3.1 10.1 - - - +
63A THR* 2.8 24.3 + - - +
82A ALA* 3.3 7.1 - - - +
83A SER* 2.9 39.6 + - - +
160A TRP* 1.3 69.0 - - - +
162A VAL* 1.3 62.5 + - - +
17B MET* 4.0 6.5 - - + -
58B GLU 4.1 14.4 - - - +
59B HIS* 2.8 30.0 + - - +
61B VAL* 4.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 4.4 3.8 - - - -
62A PHE* 2.8 29.9 + - - +
64A PHE* 3.8 28.9 - - + -
81A ILE 4.1 4.5 - - - +
82A ALA* 4.2 3.1 - - + +
160A TRP* 3.7 38.8 - - + +
161A THR* 1.3 77.0 - - - +
163A ASN* 1.3 72.0 + - - +
166A SER* 3.5 26.7 - - - +
167A LEU* 3.7 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.3 28.4 + - - +
60A ILE 3.0 15.5 - - - +
61A VAL* 4.1 8.2 - - + +
62A PHE* 4.9 0.9 - - - -
81A ILE* 5.0 2.8 + - - +
162A VAL* 1.3 76.3 - - - +
164A ALA* 1.3 58.8 + - - +
165A ARG* 3.2 11.6 + - - +
166A SER* 3.0 22.1 + - - -
167A LEU* 2.9 27.8 + - - +
83B SER* 4.4 2.2 + - - -
305C FAD 3.1 29.5 + - - -
----------------------------------------------------------
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