Contacts of the helix formed by residues 71 - 84 (chain X) in PDB entry 3RCI
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 71 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X LYS* 2.9 21.8 + - + +
70X VAL* 1.3 79.8 - - + +
72X PRO* 1.3 60.6 - - - +
73X LYS 3.3 0.2 + - - -
74X THR* 3.3 3.5 + - - -
75X ALA* 2.8 26.9 + - - +
128X GLU* 3.2 20.4 - - + +
129X ASN* 3.5 34.3 - - - +
132X LEU* 4.6 0.9 - - + -
169X VAL* 4.0 17.7 - - + -
170X VAL 3.9 4.7 - - - +
171X PHE* 3.5 36.3 - - + -
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Residues in contact with PRO 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X ALA* 3.3 30.7 - - + +
69X ASP 4.8 1.6 - - - +
70X VAL* 3.5 8.1 - - - +
71X VAL* 1.3 88.7 - - - +
73X LYS* 1.3 65.2 + - + +
75X ALA* 3.9 0.9 - - - +
76X GLU* 2.9 31.5 + - - +
128X GLU* 3.1 12.8 - - - +
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Residues in contact with LYS 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X PRO* 1.3 81.1 - - + +
74X THR* 1.3 62.4 + - - +
76X GLU* 4.6 0.2 - - - -
77X ASN* 3.2 9.9 + - - +
121X TYR* 2.6 43.2 + - + +
125X PHE* 4.6 6.7 - - + -
128X GLU* 2.8 31.0 + - + +
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Residues in contact with THR 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X VAL* 3.9 8.7 - - - -
73X LYS* 1.3 75.4 - - - +
75X ALA* 1.3 64.8 + - - +
77X ASN* 3.4 4.9 + - - +
78X PHE* 3.3 21.3 + - - +
125X PHE* 3.8 21.2 - - + -
128X GLU* 2.7 36.2 + - - +
142X MET* 3.7 27.6 - - + +
150X ASN* 6.0 0.6 - - - -
169X VAL* 4.0 9.9 - - + +
171X PHE* 3.7 27.3 - - + -
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Residues in contact with ALA 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X PRO* 5.3 2.2 - - + -
66X LEU* 3.5 25.8 - - + +
67X LYS 4.2 2.7 - - - +
68X ALA* 3.6 35.4 - - + +
71X VAL* 2.8 18.6 + - + +
72X PRO 3.9 0.7 - - - +
74X THR* 1.3 77.5 - - - +
76X GLU* 1.3 56.1 + - - +
78X PHE 3.3 1.4 + - - -
79X ARG* 2.9 29.6 + - - +
171X PHE* 4.6 8.2 - - - +
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Residues in contact with GLU 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X PRO 2.9 19.6 + - - +
73X LYS* 4.6 0.7 - - - -
74X THR 3.3 0.2 - - - -
75X ALA* 1.3 73.3 - - - +
77X ASN* 1.3 68.0 + - - +
79X ARG* 2.8 44.8 + - - +
80X ALA* 3.0 27.4 + - - +
85X GLU* 4.8 0.3 - - - +
86X LYS* 5.1 5.2 + - - -
120X ILE* 4.0 10.5 - - + +
121X TYR* 3.6 15.9 - - + +
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Residues in contact with ASN 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X LYS 3.2 14.6 + - - +
74X THR 3.6 8.9 + - - +
76X GLU* 1.3 78.1 - - - +
78X PHE* 1.3 63.8 + - - +
80X ALA* 3.9 1.7 - - - +
81X LEU* 3.0 39.1 + - - +
90X TYR* 5.0 0.8 + - - -
119X SER* 3.3 4.4 - - - -
120X ILE* 2.8 42.9 + - - +
121X TYR* 3.8 10.3 + - + -
125X PHE* 3.5 19.9 - - + -
142X MET* 4.4 8.3 - - - +
151X GLY 2.9 25.0 + - - -
152X SER* 4.5 0.4 - - - +
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Residues in contact with PHE 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X VAL* 3.7 12.8 - - + -
50X LEU* 4.7 2.5 - - + -
64X LEU* 3.8 23.3 - - + -
66X LEU* 3.7 20.9 - - + -
74X THR 3.3 5.6 + - - +
75X ALA 3.8 6.3 - - - +
77X ASN* 1.3 81.5 - - - +
79X ARG* 1.3 62.7 + - - +
81X LEU* 3.2 3.2 + - - +
82X CYS* 2.9 41.0 + - - -
90X TYR* 3.3 39.3 - + - -
140X LEU* 4.4 2.2 - - + -
142X MET* 5.4 2.9 - - - -
154X PHE* 3.6 35.2 - + + -
171X PHE* 3.5 32.3 - + + -
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Residues in contact with ARG 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X PRO* 4.2 13.9 - - + -
48X VAL* 4.2 12.3 - - + -
66X LEU* 3.7 13.4 - - + +
75X ALA 2.9 17.9 + - - +
76X GLU* 2.8 43.8 + - - +
77X ASN 3.3 0.2 - - - -
78X PHE* 1.3 77.8 - - - +
80X ALA* 1.3 67.9 + - - +
82X CYS* 3.0 6.4 + - - +
83X THR* 3.0 27.8 + - + +
85X GLU* 2.9 43.2 + - - -
205X GLN* 3.0 44.7 + - - +
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Residues in contact with ALA 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76X GLU* 3.0 17.7 + - - +
79X ARG* 1.3 95.6 - - - +
81X LEU* 1.3 58.9 + - - +
83X THR* 3.1 9.9 + - - -
84X GLY* 2.9 26.5 + - - -
85X GLU* 3.6 13.7 + - + -
86X LYS* 4.3 7.4 + - + +
88X PHE 4.4 1.0 - - - +
120X ILE* 3.9 27.6 - - + -
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Residues in contact with LEU 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X ASN* 3.0 39.6 + - - +
78X PHE 3.8 0.2 - - - +
80X ALA* 1.3 76.0 - - - +
82X CYS* 1.3 61.9 + - - +
84X GLY* 3.7 3.3 + - - -
88X PHE* 3.7 38.4 - - + +
89X GLY* 3.3 17.8 - - - -
90X TYR* 3.0 60.9 + - + +
109X PHE* 4.0 6.5 - - + -
118X LYS 4.1 3.4 - - - +
120X ILE* 4.1 9.4 - - + -
152X SER* 3.5 22.4 - - - -
203X CYS* 4.5 0.7 - - - -
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Residues in contact with CYS 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X VAL* 3.9 14.6 - - + -
49X TYR 4.5 1.1 - - - -
50X LEU* 4.1 13.5 - - - -
78X PHE* 2.9 45.9 + - - -
79X ARG 3.0 8.7 + - - +
81X LEU* 1.3 75.4 - - - +
83X THR* 1.3 63.8 + - - +
84X GLY 3.5 0.2 + - - -
90X TYR* 4.0 11.7 - - - -
203X CYS* 3.2 36.0 - - - +
204X GLY* 3.9 22.0 - - - +
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Residues in contact with THR 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X ARG* 3.0 21.9 + - - +
80X ALA* 3.1 6.4 + - - -
82X CYS* 1.3 77.5 - - - +
84X GLY* 1.3 63.0 + - - +
85X GLU* 2.7 39.6 + - - +
203X CYS 4.9 0.9 - - - +
204X GLY* 4.4 4.3 - - - -
205X GLN* 3.8 28.7 - - + +
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Residues in contact with GLY 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X ALA 2.9 6.9 + - - -
81X LEU 3.7 4.0 + - - -
82X CYS 3.3 3.6 + - - -
83X THR* 1.3 77.2 - - - +
85X GLU* 1.3 58.2 + - - +
86X LYS 3.2 3.1 - - - -
87X GLY* 2.9 24.1 + - - -
88X PHE 3.5 21.2 + - - -
89X GLY* 4.8 1.1 - - - -
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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