Contacts of the helix formed by residues 43 - 62 (chain A) in PDB entry 1RI4
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 THR 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER 3.1 2.5 + - - +
42A LYS* 1.3 82.7 - - - +
44A ILE* 1.3 62.7 + - - +
45A ASN 3.3 2.5 - - - -
46A ILE* 3.2 21.0 + - + +
47A ARG* 2.9 55.7 + - - +
193A PHE* 4.1 18.4 - - + -
216A LEU* 5.6 6.3 - - + -
217A LEU* 3.6 35.8 + - + +
218A ASP* 4.8 2.3 - - + +
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.1 24.6 + - - +
42A LYS 4.8 1.6 - - - -
43A THR* 1.3 79.1 + - - +
45A ASN* 1.3 81.7 + - - +
47A ARG* 3.1 14.9 + - + +
48A ASN* 2.9 56.7 + - - +
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Residues in contact with ASN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS 5.1 1.6 + - - -
43A THR 3.3 0.4 - - - -
44A ILE* 1.3 94.7 - - - +
46A ILE* 1.3 63.2 + - - +
48A ASN* 3.4 8.6 + - - +
49A ALA* 3.0 23.7 + - - +
269A GLY 4.1 13.3 - - - +
270A LEU* 5.5 1.4 - - - +
272A CYS 5.7 3.3 + - - -
273A LEU* 4.0 9.1 - - + +
274A THR* 5.5 1.4 - - - +
277A GLU* 2.8 39.7 + - - +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 3.2 22.3 + - + +
45A ASN* 1.3 76.3 - - - +
47A ARG* 1.3 59.6 + - + +
49A ALA* 3.5 5.6 + - - +
50A ASN* 3.1 42.0 + - - +
193A PHE* 3.7 39.0 - - + -
216A LEU* 5.3 8.3 - - + -
273A LEU* 4.8 0.4 - - - -
277A GLU* 4.0 26.9 - - + +
280A VAL* 4.0 33.9 - - + -
281A VAL* 4.1 11.7 - - + -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER 4.7 9.1 - - - +
43A THR* 2.9 37.7 + - - +
44A ILE* 3.6 14.4 - - + +
46A ILE* 1.3 75.2 - - + +
48A ASN* 1.3 67.9 + - - +
50A ASN* 3.4 6.9 + - - +
51A ASN* 3.0 37.0 + - - +
217A LEU 4.8 0.6 + - - -
218A ASP* 3.0 41.8 + - - +
219A SER* 6.0 0.4 - - - -
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 2.9 50.0 + - - +
45A ASN* 3.7 7.6 + - - +
47A ARG* 1.3 78.1 - - - +
49A ALA* 1.3 57.4 + - - +
51A ASN* 3.4 6.6 + - - +
52A PHE* 2.8 30.8 + - - +
268A MET* 4.6 11.4 - - + +
269A GLY* 3.1 45.6 + - - +
270A LEU* 3.9 8.0 - - + +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN 3.0 16.9 + - - +
46A ILE 3.6 5.2 - - - +
48A ASN* 1.3 76.7 - - - +
50A ASN* 1.3 58.6 + - - +
52A PHE* 3.2 2.5 + - - +
53A ILE* 2.8 35.9 + - + +
254A TYR* 4.2 17.5 - - + -
270A LEU* 3.9 11.8 - - + +
273A LEU* 4.2 18.2 - - + -
281A VAL* 4.4 14.4 - - + -
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.1 33.0 + - - +
47A ARG* 3.9 6.6 - - - +
48A ASN 3.4 0.2 - - - -
49A ALA* 1.3 79.5 - - - +
51A ASN* 1.3 58.3 + - - +
53A ILE* 3.5 6.1 + - - +
54A LYS* 3.0 36.1 + - - +
141A PHE* 4.0 27.7 - - + -
216A LEU* 6.2 1.4 - - - +
250A PHE* 3.1 27.1 - - - -
280A VAL* 6.0 0.4 - - - +
281A VAL* 4.5 9.4 - - - +
284A TYR* 5.0 7.4 - - - -
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.0 30.0 + - - +
48A ASN* 3.8 7.1 + - - +
50A ASN* 1.3 74.4 - - - +
52A PHE* 1.3 60.6 + - - +
54A LYS* 3.2 14.8 + - - +
55A ALA* 2.8 25.8 + - - +
77A GLY 4.3 2.6 - - - +
81A LYS* 2.7 41.3 + - - +
268A MET* 4.5 7.9 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN 2.8 19.3 + - - +
49A ALA 3.3 3.1 - - - +
51A ASN* 1.3 74.0 - - - +
53A ILE* 1.3 71.2 + - + +
55A ALA* 2.8 15.6 + - + +
56A CYS* 2.8 39.1 + - - +
254A TYR* 3.8 38.1 - + - -
257A GLU* 4.4 4.3 - - + -
258A GLY* 4.2 19.7 - - - -
264A LEU* 4.6 12.6 - - + -
265A SER* 4.5 16.4 - - - -
268A MET* 3.6 28.4 - - + +
270A LEU* 3.8 31.2 - - + -
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 2.8 22.8 + - - +
50A ASN* 3.9 4.3 - - - +
52A PHE* 1.3 79.5 - - + +
54A LYS* 1.3 58.2 + - - +
56A CYS* 3.4 1.5 + - - -
57A LEU* 2.9 28.2 + - + +
173A THR* 4.9 4.7 - - + -
250A PHE* 3.4 71.3 - - + +
253A PHE* 3.6 30.8 - - + -
254A TYR* 4.0 23.1 - - + -
281A VAL* 4.5 4.5 - - + -
286A VAL* 4.5 4.5 - - + -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN* 3.0 19.1 + - - +
51A ASN* 3.4 23.6 + - - +
53A ILE* 1.3 78.4 - - - +
55A ALA* 1.3 59.2 + - - +
57A LEU* 3.4 4.9 + - - +
58A ILE* 2.9 36.6 + - + +
77A GLY 5.6 0.2 + - - -
78A ASP* 3.0 29.8 - - - +
81A LYS* 4.0 3.6 - - - -
140A GLN* 3.5 30.7 - - + +
141A PHE* 3.6 30.0 - - + -
173A THR* 5.3 0.2 - - + -
299A SAM 2.8 35.7 + - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASN 2.8 12.3 + - - +
52A PHE* 2.8 11.8 + - + +
54A LYS* 1.3 73.9 - - - +
56A CYS* 1.3 62.8 + - - +
58A ILE* 3.6 4.6 - - - +
59A ARG* 2.8 32.1 + - - +
81A LYS* 3.8 23.3 - - + +
84A ARG* 5.3 4.7 - - - +
268A MET* 4.5 11.4 - - + -
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Residues in contact with CYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 2.8 53.4 + - - +
53A ILE 3.7 4.5 - - - +
55A ALA* 1.3 76.2 - - - +
57A LEU* 1.3 61.3 + - - +
59A ARG* 3.3 10.4 + - - +
60A LEU* 2.9 35.5 + - - +
253A PHE* 3.9 15.9 - - + -
257A GLU* 3.9 22.0 - - + +
264A LEU* 5.2 9.6 - - - -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 2.9 18.3 + - + +
54A LYS 3.8 4.5 - - - +
56A CYS* 1.3 76.2 - - - +
58A ILE* 1.3 62.9 + - - +
60A LEU* 3.3 10.0 + - + -
61A TYR* 3.4 40.6 + - + +
140A GLN* 4.0 17.3 - - - +
171A ILE* 4.1 20.2 - - + +
172A MET 4.2 3.1 - - - +
173A THR* 4.0 21.8 - - + -
246A GLU* 6.1 0.4 - - + -
253A PHE* 4.2 15.2 - - + -
286A VAL* 3.4 36.1 - - + -
288A VAL* 4.1 8.1 - - + -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 2.9 27.2 + - + +
55A ALA* 3.6 5.4 - - - +
57A LEU* 1.3 76.1 - - + +
59A ARG* 1.3 59.7 + - - +
62A THR* 2.6 49.3 + - + +
78A ASP* 4.0 9.6 - - - +
81A LYS* 3.9 31.4 - - + +
82A TYR* 3.4 56.1 - - + +
85A ALA* 4.4 9.6 - - + -
138A SER* 5.4 0.9 - - - +
140A GLN* 5.6 1.3 - - + +
171A ILE* 4.4 12.3 - - + -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA 2.8 18.7 + - - +
56A CYS* 3.8 9.4 - - - +
58A ILE* 1.3 79.3 - - + +
60A LEU* 1.3 68.9 + - - +
61A TYR 3.6 0.2 + - - -
62A THR* 3.9 15.1 - - - +
85A ALA* 5.5 4.3 - - + -
261A ASN* 4.8 14.6 - - - +
264A LEU* 3.3 37.7 - - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A CYS 2.9 20.2 + - - +
57A LEU* 3.6 7.0 - - - +
58A ILE 3.2 0.8 - - - -
59A ARG* 1.3 84.8 - - - +
61A TYR* 1.3 80.3 + - + +
62A THR 5.1 0.2 - - - -
253A PHE* 4.0 16.4 - - + -
257A GLU* 3.3 35.2 - - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.4 38.9 + - + +
60A LEU* 1.3 96.9 - - + +
62A THR* 1.3 65.5 + - + +
63A LYS 4.4 0.2 + - - -
66A ASP* 4.4 1.4 - - - +
136A VAL* 3.5 17.3 - - + +
169A TYR* 3.4 59.0 - + + -
171A ILE* 4.2 16.6 - - + -
245A VAL* 4.4 3.9 + - + +
246A GLU* 3.7 28.9 + - + +
288A VAL* 3.9 12.0 - - + +
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 2.6 37.1 + - + +
59A ARG* 3.9 11.4 - - - +
60A LEU 5.1 0.2 - - - -
61A TYR* 1.3 85.7 + - + +
63A LYS* 1.3 61.5 + - - +
66A ASP* 3.7 6.3 - - - -
68A VAL* 4.8 2.2 - - + -
82A TYR* 4.4 13.2 - - + -
85A ALA* 3.6 21.5 - - - +
87A ILE* 4.5 13.5 - - - -
136A VAL* 4.4 20.0 - - + -
171A ILE* 5.4 1.3 - - + -
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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
------------------------------------------------------------
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