Contacts of the strand formed by residues 91 - 97 (chain A) in PDB entry 1BOO
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 91 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE 4.3 1.8 - - - -
48A SER* 3.3 17.0 - - - -
87A LEU* 3.9 13.2 - - - -
88A LYS* 2.7 18.3 + - - -
89A PRO 3.2 0.4 - - - -
90A ASP* 1.3 83.2 + - - +
92A SER* 1.3 61.6 + - - -
164A SER* 3.6 2.9 - - - -
165A LYS* 3.1 26.3 + - - +
169A PRO* 4.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER 3.0 8.1 + - - -
49A LEU* 3.3 7.8 - - - +
50A VAL 2.9 24.3 + - - -
87A LEU* 3.4 8.1 - - - +
90A ASP 4.0 1.1 + - - -
91A GLY* 1.3 70.3 - - - -
93A PHE* 1.3 61.1 + - - +
94A VAL* 4.0 0.9 - - - -
162A TRP* 2.9 32.8 + - - -
163A PHE 3.4 4.6 + - - -
164A SER* 4.3 0.4 - - - +
169A PRO* 3.4 18.7 - - - +
170A LYS 4.8 0.2 + - - -
262A LEU* 3.6 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.5 35.4 - - + +
52A THR* 4.2 9.2 - - - -
76A PHE* 3.9 16.8 - + - -
79A PHE 5.5 0.2 - - - -
80A ALA* 4.1 13.2 - - - -
83A VAL* 4.0 12.6 - - + -
87A LEU* 3.9 15.2 - - + +
92A SER* 1.3 72.1 - - - +
94A VAL* 1.3 58.8 + - - +
95A VAL* 3.5 22.9 - - + -
119A MET* 3.2 35.4 - - + -
125A PHE* 3.7 20.9 - + + -
163A PHE* 2.9 41.4 + + + +
272A ILE* 4.6 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.6 23.6 - - + -
50A VAL 3.1 10.2 + - - +
51A MET* 3.5 15.4 - - + +
52A THR 3.2 24.0 + - - +
92A SER* 4.6 0.2 - - - -
93A PHE* 1.3 72.3 - - - +
95A VAL* 1.3 63.6 + - - +
96A ASP 4.3 0.2 - - - -
160A VAL* 3.8 25.4 - - + -
161A TRP 3.3 7.9 - - - +
162A TRP* 4.1 13.9 - - + -
258A PHE* 3.8 33.9 - - + -
262A LEU* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET* 5.9 0.2 - - - -
52A THR* 3.4 4.0 - - - +
54A PRO* 3.8 17.5 - - + -
76A PHE* 4.2 5.8 - - + -
93A PHE* 3.5 36.6 - - + -
94A VAL* 1.3 77.6 - - - +
96A ASP* 1.3 62.0 + - - +
97A PHE* 3.4 36.8 - - + -
159A THR 3.6 2.4 - - - +
160A VAL* 3.4 4.5 - - - -
161A TRP* 2.9 33.6 + - + +
163A PHE* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET* 5.4 2.6 - - + +
52A THR 2.8 12.4 + - - +
53A SER* 3.1 45.0 + - - -
54A PRO* 3.3 11.8 - - - +
95A VAL* 1.3 71.2 - - - +
97A PHE* 1.3 67.4 + - - +
133A TRP* 3.6 26.1 - - - -
158A ASN* 3.6 28.1 - - - +
159A THR 4.2 2.0 - - - -
160A VAL* 4.0 12.7 - - + +
250A PHE* 3.8 8.2 - - + +
254A LEU* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO* 4.1 17.9 - - + -
56A PHE* 6.0 0.7 - - + -
72A TYR* 4.1 13.7 - + - -
76A PHE* 4.3 11.0 - + - -
95A VAL* 3.4 27.8 - - + -
96A ASP* 1.3 77.5 + - - +
98A GLY* 1.3 58.7 + - - +
111A TYR* 3.7 27.6 - + - +
112A ASN* 3.7 13.2 - - + -
115A VAL* 3.9 31.9 - - + -
158A ASN* 3.1 9.9 - - - +
159A THR* 3.1 42.9 + - - +
161A TRP* 3.8 31.9 - + - -
163A PHE* 5.5 0.2 - + - -
----------------------------------------------------------
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