Contacts of the strand formed by residues 102 - 106 (chain A) in PDB entry 1YTB
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 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.4 48.2 - - + +
85A VAL* 4.2 16.8 - - + -
86A ALA* 4.0 7.0 - - + -
92A ALA* 3.8 24.7 - - + -
93A GLU 3.4 11.7 - - - +
94A TYR* 3.9 10.5 - - + -
101A ALA* 1.3 73.8 - - - +
103A ILE* 1.3 65.7 + - - +
104A MET* 3.6 7.2 + - + +
113A ALA 3.4 3.1 - - - +
114A LEU* 3.5 2.4 - - - -
115A ILE* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN 3.9 0.7 - - - +
92A ALA* 3.4 2.1 - - - -
93A GLU* 2.9 50.7 + - + +
94A TYR* 6.4 0.2 - - - -
95A ASN* 6.0 2.7 - - - +
98A ARG* 5.7 2.9 - - - +
99A PHE* 5.2 12.1 - - + -
101A ALA 4.2 9.9 - - - +
102A VAL* 1.3 73.6 - - - +
104A MET* 1.3 58.6 + - - +
105A ARG* 3.5 29.9 + - - +
112A THR* 3.7 22.7 - - + -
113A ALA 3.4 3.4 - - - +
114A LEU* 4.0 14.4 - - + -
22C T 4.2 4.3 - - - +
23C T 3.5 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.6 26.7 - - + -
89A ALA* 3.6 23.3 - - + -
91A ASN 3.3 12.1 - - - +
92A ALA* 4.3 0.9 - - + +
102A VAL* 3.6 6.6 - - + -
103A ILE* 1.3 72.6 - - - +
105A ARG* 1.3 74.1 + - - +
112A THR* 3.5 0.5 - - - +
113A ALA 2.8 32.8 + - - +
115A ILE* 3.5 31.0 - - + -
139A TYR* 3.6 26.5 + - + +
142A ILE* 3.9 27.6 - - + -
143A ILE* 3.9 8.1 - - + -
146A ILE* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 3.0 51.1 + - - +
93A GLU* 3.1 29.3 + - - +
103A ILE* 3.5 24.5 + - - +
104A MET* 1.3 83.6 - - - +
106A ILE* 1.3 71.0 + - - +
111A THR 3.7 4.3 - - - +
112A THR* 3.2 20.6 + - - +
139A TYR* 3.4 5.8 - - - -
142A ILE* 5.5 0.2 - - - +
23C T 3.7 13.3 + - - -
24C A 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 5.3 1.6 - - - +
105A ARG* 1.3 80.9 - - - +
107A ARG* 1.3 64.1 + - - +
108A GLU 3.8 15.5 - - - +
109A PRO 3.4 12.8 - - - +
110A LYS* 3.6 4.2 - - - +
111A THR* 3.2 36.3 + - - +
135A ALA* 3.7 29.4 - - + +
138A LYS* 4.0 12.8 - - + -
139A TYR* 3.2 20.3 + - + +
142A ILE* 3.7 24.2 - - + -
----------------------------------------------------------
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