Contacts of the strand formed by residues 102 - 107 (chain A) in PDB entry 3DBD
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 PHE 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.7 31.6 - - + -
91A HIS* 3.4 51.1 + + + +
92A LYS* 3.7 35.3 - - + +
94A LEU 4.9 6.9 + - - +
100A VAL 3.5 2.6 + - - -
101A GLY* 1.3 73.5 - - - -
103A HIS* 1.3 67.1 + - - +
104A GLY* 3.4 35.7 - - - -
105A PHE* 3.8 18.2 - + + -
114A VAL* 3.7 21.1 - - + -
115A VAL 4.3 1.6 - - - -
116A LEU* 3.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 6.1 0.7 - - - +
39A TYR* 4.8 6.1 + - - +
65A PHE* 3.5 40.0 - + + -
101A GLY* 3.5 27.6 + - - -
102A PHE* 1.3 74.7 + - - +
104A GLY* 1.3 63.4 + - - +
115A VAL* 3.1 25.3 + - + +
117A GLU* 4.4 12.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 6.4 1.8 - - - -
92A LYS* 5.9 0.7 - - - -
102A PHE* 3.4 19.3 - - - -
103A HIS* 1.3 76.6 - - - +
105A PHE* 1.3 61.7 + - - -
106A PHE* 4.6 2.3 - - - -
115A VAL* 3.2 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 5.6 0.3 - - - +
34A ARG* 6.0 1.7 - - - +
84A MET* 5.8 2.0 - - + -
88A ILE* 3.6 42.2 - - + -
92A LYS* 6.1 0.9 - - + -
102A PHE* 3.8 15.8 - + + -
104A GLY* 1.3 75.0 - - - -
106A PHE* 1.3 79.8 + - - +
107A GLU* 5.1 9.0 - - + -
112A VAL* 4.4 11.0 - - + -
113A TYR 3.3 12.1 - - - +
114A VAL* 4.1 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.3 14.4 - - + -
31A VAL 3.8 17.3 - - - -
32A ASP* 3.3 37.7 - - + +
33A PRO* 4.8 4.7 - - + -
34A ARG* 6.0 2.9 - - + -
39A TYR* 4.0 26.0 - + - -
56A ILE* 6.1 0.4 - - + -
104A GLY 4.6 2.0 - - - -
105A PHE* 1.3 88.3 - - - +
107A GLU* 1.3 67.1 + - - +
112A VAL* 3.5 4.3 - - - +
113A TYR* 2.7 75.1 + + + +
115A VAL* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 5.9 0.4 - - - -
33A PRO* 4.5 17.4 - - - +
72A LYS* 3.2 33.9 + - - +
84A MET* 5.9 0.7 - - - +
105A PHE* 5.1 8.9 - - + -
106A PHE* 1.3 87.1 - - - +
108A ASP* 1.3 59.4 + - - +
111A PHE 3.5 8.5 - - - +
112A VAL* 3.9 17.0 - - + +
113A TYR* 4.5 0.4 - - - -
----------------------------------------------------------
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