Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 1Y7M
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 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PRO 5.2 0.7 - - - +
54B ILE* 3.2 18.3 - - + +
55B PRO* 1.3 88.0 - - + +
57B HIS* 1.3 63.1 + - - +
69B LEU* 4.0 19.1 - - + -
70B SER 3.1 16.4 - - - +
71B LEU* 3.9 30.6 - - + +
76B MSE 4.2 8.8 - - - +
153B ILE* 3.5 40.7 + - + +
154B VAL* 4.1 10.5 - - + -
155B PRO* 3.9 21.8 - - + -
158B THR* 3.8 16.9 - - + +
159B ARG* 4.6 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 4.7 11.7 + - - -
52A TYR* 4.0 23.2 - + - -
55B PRO 5.3 0.9 - - - +
56B TYR* 1.3 75.1 - - - +
58B ILE* 1.3 83.6 + - - +
59B ALA* 4.1 9.2 + - + +
68B THR 3.8 0.9 - - - +
69B LEU* 3.7 1.1 - - - -
70B SER* 2.9 42.7 + - - +
73B ASN* 4.6 16.0 + - - +
159B ARG* 3.6 27.9 - - + -
161B THR* 2.8 30.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 1.3 84.6 + - - +
59B ALA* 1.3 62.1 + - - +
60B VAL* 4.2 2.0 - - + -
67B LEU* 3.6 33.4 - - + -
68B THR 3.2 5.8 - - - +
69B LEU* 4.0 15.3 - - + -
97B ILE* 4.6 6.1 - - + -
122B ILE* 5.1 1.1 - - + -
150B LEU* 4.0 28.9 - - + -
154B VAL* 4.2 11.4 - - + -
158B THR* 4.2 14.8 - - + -
159B ARG 2.9 12.2 + - - +
160B VAL* 4.0 29.8 - - + -
161B THR 2.8 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.8 26.1 + - + +
42A SER* 4.8 6.1 - - - +
57B HIS* 4.1 12.7 + - + +
58B ILE* 1.3 74.8 - - - +
60B VAL* 1.3 62.4 + - - +
66B THR 4.0 0.9 - - - +
67B LEU* 3.6 1.0 - - - -
68B THR* 2.9 40.2 + - + +
70B SER* 6.1 0.4 - - - +
161B THR* 3.3 7.4 - - - +
163B ASN* 4.9 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.1 9.5 + - - +
58B ILE* 4.2 7.2 - - + -
59B ALA* 1.3 76.0 - - - +
61B SER* 1.3 65.5 + - - +
62B ILE* 4.5 4.9 - - + +
66B THR 3.4 2.9 - - - -
67B LEU* 3.8 30.1 - - + -
81B ILE* 3.7 22.9 - - + -
83B VAL* 5.5 0.2 - - + -
140B ILE* 3.9 20.2 - - + -
160B VAL* 4.3 7.2 - - + -
161B THR 2.7 15.0 + - - +
162B ILE* 3.9 20.6 - - + -
163B ASN 2.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.2 21.3 + - - +
6A VAL 5.1 1.6 + - - -
7A LYS* 5.4 2.9 - - - -
8A GLN* 5.2 3.1 + - - +
40A GLY* 4.0 6.7 + - - -
60B VAL* 1.3 73.5 - - - +
62B ILE* 1.3 58.4 + - - +
63B GLY* 4.5 0.2 - - - -
64B ALA* 3.4 22.7 + - - +
65B LYS* 2.9 23.6 + - - -
66B THR* 2.9 32.2 + - - +
81B ILE* 4.3 1.9 - - - +
163B ASN* 3.7 4.0 - - - -
164B ARG 3.8 11.7 + - - -
----------------------------------------------------------
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