Contacts of the strand formed by residues 59 - 72 (chain B) in PDB entry 1RM1
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 LYS 59 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN 3.6 11.0 + - - +
58B SER* 1.3 81.0 - - - +
60B LEU* 1.3 62.7 + - - +
61B THR* 4.7 4.5 - - + +
86B THR 4.5 0.7 - - - +
87B VAL 4.6 0.7 - - - +
88B GLU 3.9 22.4 + - - +
276C PHE* 4.6 0.2 - - - -
277C GLN* 4.3 7.9 - - + -
278C LYS* 3.0 51.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 4.2 0.9 - - - -
59B LYS* 1.3 73.5 - - - +
61B THR* 1.3 70.9 + - - +
62B VAL* 3.8 16.2 - - + -
85B VAL* 4.2 12.6 - - + -
86B THR 3.1 17.5 - - - +
87B VAL* 4.0 16.2 - - + +
244C MET* 3.8 21.1 - - + -
267C VAL* 3.9 20.2 - - + -
269C ILE* 5.4 0.4 - - + -
274C TYR* 4.6 10.8 - - + -
275C THR 5.5 0.4 - - - +
276C PHE* 3.9 30.2 - - + +
278C LYS 3.0 7.0 + - - +
279C ALA* 3.0 31.7 - - + -
280C GLN* 3.0 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LYS 4.7 4.0 - - - +
60B LEU* 1.3 85.0 - - - +
62B VAL* 1.3 65.7 + - - +
63B LYS* 5.1 12.9 - - - +
84B GLN 3.5 2.1 + - - +
85B VAL* 3.4 4.3 - - - +
86B THR* 2.6 48.6 + - - +
280C GLN* 3.1 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.8 18.8 - - + -
61B THR* 1.3 76.2 - - - +
63B LYS* 1.3 63.2 + - - +
80B VAL* 4.3 11.7 - - + -
83B CYS* 4.0 26.9 - - + -
84B GLN 3.7 2.0 - - - -
85B VAL* 4.3 14.4 - - + -
111B LEU* 4.6 11.9 - - + -
113B ILE* 4.8 0.9 - - + -
244C MET* 4.2 14.8 - - + -
280C GLN 2.6 11.8 + - - +
281C VAL* 3.2 23.8 - - + +
282C GLU* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 5.1 12.6 - - - +
62B VAL* 1.3 82.2 - - - +
64B GLY* 1.3 58.5 + - - +
83B CYS* 2.9 4.6 - - - +
84B GLN* 2.7 49.2 + - + +
280C GLN 5.7 0.2 - - - +
282C GLU* 3.3 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL 4.3 0.2 - - - -
63B LYS* 1.3 75.8 - - - +
65B ASN* 1.3 66.0 + - - -
80B VAL* 3.9 4.2 - - - +
82B ASN 3.8 7.6 - - - -
83B CYS* 3.5 14.1 - - - -
282C GLU 3.2 7.7 + - - +
283C ALA* 2.9 24.1 - - - +
284C GLU* 3.2 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY* 1.3 77.1 - - - -
66B LEU* 1.3 60.0 + - - +
67B ASP* 3.1 5.2 + - + -
80B VAL* 3.5 1.4 - - - -
81B LYS* 2.9 44.4 + - + +
82B ASN* 4.0 13.3 - - - +
283C ALA* 4.1 1.3 - - - -
284C GLU* 3.7 24.5 + - - +
286C VAL* 4.3 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 2.9 20.4 + - - -
65B ASN* 1.3 69.0 - - - +
67B ASP* 1.3 60.3 + - - +
68B THR 2.8 31.6 - - - +
69B TYR* 3.8 21.1 - - + -
78B PHE* 4.2 15.0 - - + -
79B ILE 3.7 11.4 - - - +
80B VAL* 4.6 2.9 - - + +
258C TRP* 3.7 39.0 - - + +
283C ALA* 3.4 25.4 - - + +
284C GLU 3.2 6.9 + - - +
285C TRP* 3.2 27.8 - - + +
286C VAL 4.2 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 5.1 4.5 + - - -
91A ASN* 4.0 2.4 + - - +
107A ARG* 3.4 29.6 + - - +
65B ASN* 3.1 4.8 + - - +
66B LEU* 1.3 73.4 - - - +
68B THR* 1.3 70.5 + - - +
79B ILE* 2.8 26.4 + - + +
81B LYS* 3.8 44.2 + - + +
285C TRP* 3.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 3.9 45.3 + - + +
91A ASN* 3.4 12.3 + - - +
66B LEU* 2.8 17.6 - - - +
67B ASP* 1.3 93.1 + - - +
69B TYR* 1.3 77.0 + - - +
77B THR 4.5 0.4 - - - -
78B PHE* 3.4 0.9 - - - -
79B ILE* 2.9 35.7 + - + +
231C ILE* 4.7 5.4 - - + -
285C TRP* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 4.7 0.2 - - - -
91A ASN* 2.8 76.3 + - + -
92A ALA 3.9 5.2 - - - -
93A GLU* 4.0 16.2 - - + -
103A ILE 4.9 0.5 + - - -
104A MET* 4.7 0.3 - - - -
105A ARG* 2.8 39.1 + - - +
66B LEU* 3.8 6.3 - - + -
68B THR* 1.3 81.4 - - - +
70B GLY* 1.3 64.6 + - - +
76B TRP* 4.4 5.6 - + - -
77B THR* 3.2 9.4 - - - -
78B PHE* 3.7 22.0 - - + -
231C ILE* 5.7 0.7 - - - +
258C TRP* 3.6 27.8 - + + -
285C TRP* 3.8 27.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 3.4 11.2 - - - -
69B TYR* 1.3 80.6 - - - +
71B PHE* 1.3 62.3 + - - -
72B CYS 4.2 0.4 - - - -
75B VAL 3.5 1.0 - - - +
76B TRP* 3.3 10.6 - - - -
77B THR* 2.9 36.7 + - - -
231C ILE* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 5.1 0.5 - - - +
92A ALA 3.0 8.8 + - - +
93A GLU* 3.2 20.4 - - + +
94A TYR 2.8 42.6 + - - -
95A ASN* 3.5 37.9 - - + -
70B GLY* 1.3 75.3 - - - +
72B CYS* 1.3 61.6 + - - +
74B ASP* 3.7 31.2 - - - -
75B VAL 3.2 14.4 - - - -
76B TRP* 3.3 47.1 - + + -
248C TYR* 3.7 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 4.1 17.5 - - - -
86A ALA* 3.7 27.4 - - + +
87A LEU* 3.5 31.9 - - + -
92A ALA 5.9 0.2 - - - +
94A TYR* 4.0 14.8 - - - -
70B GLY 4.2 0.4 - - - -
71B PHE* 1.3 75.8 - - - +
73B ASP* 1.3 76.4 + - - +
74B ASP 3.2 2.9 - - - +
75B VAL* 3.0 22.3 + - - +
----------------------------------------------------------
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