Contacts of the strand formed by residues 75 - 86 (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 VAL 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B GLY 3.5 1.0 - - - +
71B PHE* 3.2 11.5 - - - -
72B CYS 3.0 30.5 + - - +
73B ASP* 3.7 11.7 - - + +
74B ASP* 1.3 85.2 - - - +
76B TRP* 1.3 69.0 + - - +
77B THR* 4.1 9.2 + - - +
114B VAL* 4.0 18.4 - - + -
115B ALA 3.5 8.7 - - - +
116B CYS* 4.2 20.0 - - - -
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Residues in contact with TRP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 3.8 20.0 - - - -
69B TYR* 4.4 6.3 - + - -
70B GLY 3.3 19.7 - - - -
71B PHE* 3.3 41.7 - + + -
75B VAL* 1.3 72.2 - - - +
77B THR* 1.3 63.6 + - - +
78B PHE* 3.3 39.8 - + + -
113B ILE 3.6 0.9 - - - +
114B VAL* 3.4 3.1 - - - -
115B ALA* 2.8 38.8 + - + +
248C TYR* 3.4 40.7 - + + -
251C VAL* 3.7 28.7 - - + +
258C TRP* 3.7 31.9 - + - -
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B THR 4.0 0.6 - - - +
69B TYR* 3.2 6.1 - - - -
70B GLY* 2.9 39.5 + - - -
75B VAL* 4.1 12.6 + - - +
76B TRP* 1.3 77.0 + - - +
78B PHE* 1.3 68.3 + - - +
79B ILE* 5.4 3.1 - - + -
112B ARG* 4.3 24.0 - - + +
113B ILE 3.2 7.9 - - - +
114B VAL* 4.2 16.8 - - + +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.2 14.4 - - + -
68B THR 3.4 3.6 - - - +
69B TYR* 3.7 19.5 - - + -
76B TRP* 3.3 56.8 - + + -
77B THR* 1.3 81.1 - - - +
79B ILE* 1.3 63.8 + - - +
80B VAL* 3.9 6.7 - - + -
111B LEU 3.5 1.0 - - - +
112B ARG* 3.4 4.0 - - - +
113B ILE* 2.7 67.2 + - + +
115B ALA* 5.8 2.0 - - + -
248C TYR* 6.4 0.2 - - + -
251C VAL* 4.0 8.5 - - + -
258C TRP* 4.1 12.1 - + + -
260C CYS* 3.6 32.5 - - + -
262C LEU* 5.6 4.0 - - + -
281C VAL* 6.1 2.2 - - + -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 4.0 24.9 - - - +
66B LEU* 3.7 1.7 - - - +
67B ASP* 2.8 44.4 + - + +
68B THR* 2.9 29.5 + - + +
77B THR* 5.4 3.4 - - + -
78B PHE* 1.3 78.3 - - - +
80B VAL* 1.3 59.7 + - - +
81B LYS* 4.4 4.3 - - + -
110B LYS* 3.9 36.8 - - + +
111B LEU 3.5 4.0 - - - +
112B ARG* 3.9 34.5 - - + +
232C SER* 5.5 0.9 - - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 4.3 7.2 - - + -
64B GLY* 3.9 13.5 - - - +
65B ASN 3.5 10.8 - - - +
66B LEU* 4.9 2.5 - - + -
78B PHE* 4.7 8.5 - - + -
79B ILE* 1.3 75.3 - - - +
81B LYS* 1.3 62.7 + - - +
83B CYS* 3.4 35.3 - - + -
110B LYS* 3.3 2.1 - - - -
111B LEU* 2.7 48.0 + - + +
113B ILE* 4.4 20.9 - - + -
281C VAL* 4.5 8.3 - - + -
283C ALA* 4.3 16.8 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLY 4.1 0.3 - - - -
65B ASN* 2.9 33.8 + - + +
67B ASP* 3.8 39.9 + - + +
79B ILE* 4.4 5.4 - - + -
80B VAL* 1.3 77.1 - - - +
82B ASN* 1.3 84.4 + - - +
83B CYS 3.4 2.6 + - - -
109B ASP 3.4 12.8 - - - +
110B LYS* 4.3 26.3 - - + +
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLY* 3.8 7.8 - - - -
65B ASN* 4.0 13.7 + - - +
81B LYS* 1.3 87.6 - - - +
83B CYS* 1.3 58.1 + - - +
84B GLN* 5.8 0.2 - - - +
108B VAL 3.5 7.1 + - - -
109B ASP* 3.0 21.3 + - - +
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Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 4.0 14.6 - - + -
63B LYS 2.9 19.7 - - - +
64B GLY* 3.5 1.1 - - - -
80B VAL* 3.4 42.8 - - + -
82B ASN* 1.3 76.3 - - - +
84B GLN* 1.3 61.7 + - - +
85B VAL* 4.0 3.8 + - - -
106B ILE 3.7 0.5 - - - +
107B SER* 3.7 3.3 - - - -
108B VAL* 3.0 53.3 + - - -
111B LEU* 4.3 8.7 - - - -
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 3.5 5.2 + - - +
63B LYS* 2.7 40.8 + - + +
83B CYS* 1.3 75.8 - - - +
85B VAL* 1.3 62.0 + - - +
86B THR* 3.8 6.7 + - + +
105B VAL* 3.7 22.3 - - + +
106B ILE 3.4 12.1 + - - -
107B SER* 3.5 20.8 + - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.2 25.1 - - + -
61B THR 3.4 8.1 - - - +
62B VAL* 4.3 12.3 - - + -
83B CYS* 4.4 11.4 - - - -
84B GLN* 1.3 76.3 - - - +
86B THR* 1.3 60.5 + - - +
87B VAL* 4.7 0.9 - - + -
105B VAL 3.3 0.2 - - - -
106B ILE* 2.4 54.7 + - + +
108B VAL* 3.6 28.5 - - + -
111B LEU* 5.3 5.4 - - + -
244C MET* 5.7 0.9 - - + -
269C ILE* 3.7 28.3 - - + -
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS 4.5 0.2 - - - +
60B LEU* 3.1 22.2 - - - +
61B THR* 2.6 40.0 + - - +
84B GLN* 4.8 8.3 - - + +
85B VAL* 1.3 75.7 - - - +
87B VAL* 1.3 65.5 + - - +
105B VAL* 3.4 37.7 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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