Contacts of the strand formed by residues 87 - 95 (chain A) in PDB entry 3RPF
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 SER 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.7 5.7 - - - +
9A LEU* 3.0 33.5 + - - +
11A THR* 3.1 35.9 + - - +
34A VAL* 3.5 15.0 - - - +
35A GLY 3.4 10.8 - - - -
36A ILE* 4.0 8.0 - - - +
78A SER* 3.4 2.4 + - - -
82A VAL* 3.8 1.0 - - - +
85A GLY 5.1 0.9 + - - -
86A GLN* 1.3 76.0 - - - +
88A SER* 1.3 60.1 + - - +
89A PHE 3.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.6 6.1 - - - -
35A GLY 2.9 10.5 + - - -
36A ILE 5.2 0.2 - - - -
37A VAL* 4.2 15.1 + - - +
46A LEU* 5.3 0.5 - - - +
48A PHE* 3.5 25.7 - - - -
77A HIS* 3.3 8.8 + - - -
78A SER* 2.8 33.9 + - - -
82A VAL* 4.2 3.6 - - - -
86A GLN 4.0 0.4 + - - -
87A SER* 1.3 73.7 - - - +
89A PHE* 1.3 60.4 + - - +
74D GLY 2.5 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.4 4.3 - - - +
33A PHE* 3.7 35.9 - + - -
34A VAL* 3.5 5.0 - - - +
35A GLY 2.9 27.2 + - - +
75A MSE 3.8 14.4 - - + -
76A ALA 3.5 12.8 - - - -
77A HIS* 3.7 16.6 - + + -
88A SER* 1.3 83.9 + - - +
90A LEU* 1.3 77.5 + - - +
91A CYS* 3.8 24.9 - - + -
108A PHE* 4.2 5.4 - + - -
109A ILE* 5.0 8.3 - - + -
112A PHE* 3.8 33.9 - + + -
74D GLY* 3.5 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.9 12.8 - - + -
11A THR* 4.2 22.0 - - + -
14A LEU* 4.5 11.9 - - + -
15A LEU* 4.1 21.5 - - + -
18A TYR* 3.1 39.9 - - + +
32A VAL* 4.6 3.8 - - + -
33A PHE 3.2 11.2 - - - +
34A VAL* 3.7 21.8 - - + -
75A MSE 3.3 3.6 - - - +
76A ALA* 2.9 33.8 + - + +
89A PHE* 1.3 79.9 - - - +
91A CYS* 1.3 72.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS 3.8 0.2 - - - +
32A VAL* 3.3 6.6 - - - +
33A PHE* 2.9 50.9 + - - +
73A LEU* 5.2 2.0 - - + -
74A LYS 3.3 12.8 - - - +
75A MSE 3.9 9.4 - - + -
89A PHE* 3.8 19.7 - - + -
90A LEU* 1.3 81.4 - - - +
92A VAL* 1.3 63.3 + - - +
105A TYR* 4.8 5.6 - - - -
108A PHE* 4.0 20.4 - - + -
109A ILE* 4.1 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.9 31.4 - - + -
30A PHE* 3.6 36.6 - - + -
31A CYS 3.2 11.0 - - - +
32A VAL* 4.4 3.6 - - + -
72A VAL 4.1 0.2 - - - -
73A LEU* 3.2 9.8 - - - +
74A LYS* 2.9 43.3 + - + +
91A CYS* 1.3 76.4 - - - +
93A SER* 1.3 68.6 + - - +
94A MSE 4.0 16.6 - - + -
105A TYR* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS* 2.9 34.3 + - - +
71A VAL* 3.3 17.5 - - - +
72A VAL 3.4 4.9 - - - -
73A LEU* 4.0 13.7 - - - -
92A VAL* 1.3 74.3 - - - +
94A MSE 1.3 60.4 + - - +
101A ALA* 2.7 29.7 + - - +
104A LEU* 4.1 2.1 - - - +
105A TYR* 4.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.6 29.4 - - + +
21A GLU* 3.8 22.4 - - - +
22A ALA* 3.8 20.9 - - - -
27A PHE* 3.7 17.9 - - + -
29A ALA 3.1 14.4 - - - +
30A PHE* 4.0 18.8 - - + -
71A VAL* 3.4 7.3 - - - +
72A VAL* 2.9 56.4 + - + +
74A LYS* 4.7 1.6 - - + -
92A VAL* 4.0 22.4 - - + -
93A SER* 1.3 76.0 + - - +
95A GLY* 1.3 58.8 + - - +
101A ALA* 4.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.3 18.8 - - - +
28A GLY 2.9 20.3 + - - -
29A ALA* 3.0 14.1 + - - -
70A GLY 3.9 12.1 - - - -
71A VAL* 4.7 3.8 - - - -
94A MSE 1.3 77.1 - - - +
96A LYS* 1.3 63.4 + - - -
97A ASN 3.4 6.1 - - - -
101A ALA* 4.4 3.4 - - - +
----------------------------------------------------------
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