Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 1IMV
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 1.3 73.0 - - - +
62A PRO* 1.3 62.4 - - - +
63A LEU* 3.0 7.5 + - - +
64A SER* 3.0 23.9 + - - -
116A LEU* 4.5 2.4 - - - +
118A SER* 5.2 1.0 + - - -
191A ALA* 3.4 29.1 - - - +
338A HIS* 3.2 18.9 + - - -
340A ALA* 4.5 0.2 - - - -
387A LEU 2.7 25.4 + - - -
388A PHE* 3.6 17.0 - - - -
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Residues in contact with PRO 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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38A VAL* 5.4 2.0 - - + +
41A PHE* 4.5 3.2 - - + -
42A GLY* 3.3 41.1 - - - +
45A LEU* 4.7 8.5 - - + -
60A LEU* 3.2 26.4 - - + +
61A SER* 1.3 88.6 - - - +
63A LEU* 1.3 52.9 + - - +
64A SER 3.3 0.2 - - - -
65A VAL* 2.8 14.1 + - + +
66A ALA* 2.8 35.1 + - - +
386A LEU* 3.9 21.5 - - + +
387A LEU 5.1 1.6 - - - +
389A ILE* 4.3 3.4 - - + +
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Residues in contact with LEU 63 (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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38A VAL* 3.9 23.8 - - + -
61A SER* 3.0 6.6 + - - +
62A PRO* 1.3 78.5 - - - +
64A SER* 1.3 57.3 + - - +
66A ALA* 4.4 3.6 - - - -
67A THR* 2.9 39.9 + - - +
102A TYR* 4.0 10.8 - - + +
105A LEU* 4.6 15.9 - - + -
106A LEU* 4.8 9.2 - - + -
109A VAL* 3.8 29.8 - - + -
116A LEU* 4.7 6.1 - - + -
118A SER* 4.5 13.2 - - - +
385A ALA* 5.6 5.2 - - + -
386A LEU 4.3 14.9 + - - +
387A LEU* 4.4 15.7 - - + -
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Residues in contact with SER 64 (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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61A SER 3.0 16.3 + - - -
63A LEU* 1.3 78.3 - - - +
65A VAL* 1.3 60.3 + - - +
67A THR* 4.6 0.4 - - - -
68A ALA* 3.4 7.4 + - - +
118A SER* 3.5 21.5 + - - -
119A ALA 3.7 6.5 - - - -
120A SER* 2.7 28.5 + - - -
189A GLY* 3.5 25.9 - - - -
190A VAL 3.8 5.8 - - - -
191A ALA* 4.5 1.5 - - - +
338A HIS* 3.3 18.5 + - - -
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Residues in contact with VAL 65 (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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41A PHE* 4.3 18.2 - - + -
45A LEU* 4.7 9.6 - - + -
62A PRO* 2.8 13.5 + - + +
64A SER* 1.3 76.7 - - - +
66A ALA* 1.3 65.0 + - - +
67A THR 3.2 1.3 - - - -
68A ALA* 3.3 6.4 + - - +
69A LEU* 3.2 23.7 + - + +
189A GLY* 4.7 5.8 - - - +
305A VAL* 4.5 13.5 - - + -
309A LEU* 4.7 6.7 - - + -
336A VAL* 4.2 23.1 - - + -
337A GLU 5.1 0.9 - - - +
338A HIS* 3.7 37.7 - - + +
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Residues in contact with ALA 66 (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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38A VAL* 3.4 34.5 - - + -
41A PHE* 3.6 26.2 - - + -
62A PRO 2.8 19.0 + - - +
63A LEU 3.8 1.8 - - - +
65A VAL* 1.3 72.9 - - - +
67A THR* 1.3 57.3 + - - +
69A LEU* 3.2 6.7 + - - +
70A SER* 3.0 29.1 + - - -
88A LEU* 4.2 8.4 - - + +
102A TYR* 3.6 2.5 - - - +
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Residues in contact with THR 67 (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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63A LEU* 2.9 21.9 + - - +
64A SER* 4.6 0.7 - - - -
66A ALA* 1.3 74.9 - - - +
68A ALA* 1.3 59.4 + - - +
70A SER* 3.5 1.7 + - - +
71A ALA* 3.0 28.2 + - + +
102A TYR* 2.6 33.1 + - + -
106A LEU* 4.1 15.4 - - + +
120A SER* 3.3 26.0 - - - +
142A TYR* 3.8 25.0 - - + +
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Residues in contact with ALA 68 (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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64A SER 3.4 11.6 + - - +
65A VAL* 3.3 11.5 + - + +
67A THR* 1.3 79.9 - - - +
69A LEU* 1.3 62.2 + - - +
71A ALA* 3.7 5.8 - - - +
72A LEU* 3.1 24.3 + - - +
120A SER* 3.8 13.4 + - - -
121A ARG 4.9 4.0 - - - +
122A ILE* 4.4 3.5 - - + +
187A LEU* 3.9 33.1 - - + +
188A LEU 4.3 8.5 - - - +
336A VAL* 6.1 0.4 - - + -
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Residues in contact with LEU 69 (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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41A PHE* 3.7 35.0 - - + -
65A VAL* 3.2 12.9 + - + +
66A ALA 3.2 8.1 + - - +
68A ALA* 1.3 78.0 - - - +
70A SER* 1.3 57.7 + - - +
72A LEU* 3.3 7.2 + - + +
73A SER* 3.0 28.2 + - - -
84A ILE* 3.8 21.6 - - + +
88A LEU* 4.3 10.3 - - + -
187A LEU* 3.6 23.6 - - + -
309A LEU* 4.5 10.1 - - + -
314A LEU* 4.1 17.0 - - + -
317A LEU* 4.5 22.2 - - + -
333A LEU* 4.6 5.2 - - + -
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Residues in contact with SER 70 (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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66A ALA 3.0 15.7 + - - -
67A THR 4.0 2.5 - - - -
69A LEU* 1.3 74.4 - - - +
71A ALA* 1.3 64.9 + - - +
73A SER* 2.5 24.3 + - - -
88A LEU* 3.9 8.9 - - - +
90A TYR* 3.0 35.0 + - - -
98A ILE* 5.5 0.2 - - - +
99A HIS* 3.5 13.2 - - - -
102A TYR* 3.8 8.7 - - - -
142A TYR* 2.7 25.8 + - - -
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Residues in contact with ALA 71 (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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67A THR* 3.0 19.3 + - + +
68A ALA* 3.7 6.7 - - - +
70A SER* 1.3 76.2 - - - +
72A LEU* 1.3 64.2 + - - +
74A LEU* 3.0 25.3 + - - +
120A SER* 6.2 0.7 - - - -
122A ILE* 4.0 9.9 - - + -
134A PHE* 4.0 4.0 - - - -
138A LEU* 3.7 25.0 - - + +
142A TYR* 3.8 24.1 - - + -
144A THR* 5.4 2.2 - - + -
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Residues in contact with LEU 72 (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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68A ALA 3.1 14.7 + - - +
69A LEU* 3.6 7.2 - - + +
71A ALA* 1.3 74.7 - - - +
73A SER* 1.3 52.2 + - - +
74A LEU 2.7 17.3 + - - -
75A GLY* 2.9 18.5 + - - -
76A ALA 3.9 0.3 + - - -
84A ILE* 5.0 5.4 - - + -
122A ILE* 3.7 30.7 - - + +
134A PHE* 4.2 1.6 - - - -
185A ILE* 4.3 17.9 - - + -
187A LEU* 4.2 22.2 - - + -
317A LEU* 5.8 0.9 - - + -
323A PHE* 3.7 29.7 - - + -
326A ILE* 3.6 28.3 - - + -
333A LEU* 4.7 9.4 - - + -
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Residues in contact with SER 73 (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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69A LEU 3.0 12.6 + - - -
70A SER* 2.5 27.0 + - - -
72A LEU* 1.3 75.3 - - - +
74A LEU* 1.3 61.9 + - - +
75A GLY 3.4 0.2 - - - -
76A ALA* 3.7 15.9 + - - +
81A GLU* 4.0 20.1 - - - +
84A ILE* 3.8 31.6 - - - +
85A HIS* 3.8 21.3 + - - -
99A HIS* 4.0 6.5 + - - -
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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