Contacts of the helix formed by residues 25 - 45 (chain C) in PDB entry 4IRV
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 GLN 25 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 1.3 77.9 - - - +
26C PHE* 1.3 56.2 + - - +
28C ASN* 3.7 6.5 - - - +
29C ASN* 2.9 49.6 + - - +
130C SER 3.9 10.6 + - - +
131C HIS* 4.4 2.8 + - - +
132C GLN 2.2 34.4 + - - -
133C LYS* 3.3 20.0 + - - +
135C PRO* 5.7 2.5 - - + -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN 4.0 7.9 - - - +
25C GLN* 1.3 79.4 - - - +
27C ILE* 1.3 84.4 + - + +
29C ASN* 3.1 4.6 + - - +
30C LEU* 2.8 46.0 + - + +
126C THR* 4.4 7.4 - - + -
130C SER* 3.7 33.4 + - - +
175C ILE* 4.1 10.3 - - + -
220C ILE 6.0 0.4 - - - -
762G MSE 3.4 37.5 - - + -
765G ILE* 4.2 29.4 - - + -
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Residues in contact with ILE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.5 16.5 + - - +
26C PHE* 1.3 90.9 - - + +
28C ASN* 1.3 71.3 + - - +
30C LEU* 3.0 4.4 + - + -
31C GLN* 2.8 46.6 + - + +
175C ILE* 4.0 30.1 - - + +
176C ILE* 4.4 9.2 - - + -
179C ASN* 3.6 49.4 - - + +
180C GLN* 5.5 0.4 - - - +
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Residues in contact with ASN 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLN* 3.5 41.9 + - - +
186A LYS* 5.2 2.7 + - - +
24C GLN* 3.0 28.0 + - - +
25C GLN* 3.7 7.1 - - - +
27C ILE* 1.3 78.4 - - - +
29C ASN* 1.3 62.2 + - - +
31C GLN* 3.4 14.5 + - - +
32C VAL* 3.3 24.3 + - - +
135C PRO* 4.4 16.0 - - + +
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Residues in contact with ASN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLN* 2.9 28.4 + - - +
26C PHE* 3.5 3.8 - - - +
28C ASN* 1.3 70.8 - - - +
30C LEU* 1.3 66.4 + - - +
32C VAL* 3.2 6.2 + - - +
33C ALA* 3.0 18.4 + - - +
129C VAL* 3.0 37.1 + - + +
130C SER 3.3 10.5 + - - -
132C GLN* 3.0 29.5 + - - +
134C ASP 4.0 0.2 - - - -
135C PRO* 3.2 33.3 - - - +
138C ILE* 3.8 13.8 - - + +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 2.8 36.2 + - + +
27C ILE* 3.5 9.0 - - - +
29C ASN* 1.3 76.5 - - - +
31C GLN* 1.3 52.9 + - - +
33C ALA* 3.1 2.8 + - - +
34C PHE* 2.8 35.3 + - - +
126C THR* 4.7 5.6 - - + +
129C VAL* 3.7 23.1 - - + -
172C PHE* 3.8 49.9 - - + -
175C ILE* 3.6 36.8 - - + -
176C ILE* 4.0 12.8 - - + -
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Residues in contact with GLN 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 4.5 2.8 - - - +
78A ILE* 4.9 0.7 - - - +
185A GLN* 6.4 0.2 - - - +
186A LYS* 3.0 52.1 - - + +
27C ILE* 2.8 35.7 + - + +
28C ASN* 3.7 13.7 + - - +
29C ASN 3.2 0.2 - - - -
30C LEU* 1.3 71.8 - - - +
32C VAL* 1.3 61.9 + - + +
34C PHE* 3.6 6.6 + - - +
35C ILE* 3.5 25.6 + - - +
63C PHE* 5.8 1.4 - - - -
176C ILE* 3.5 39.1 - - + +
180C GLN* 3.9 14.1 + - - +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 4.1 28.7 - - + -
186A LYS* 6.0 0.9 - - + -
190A VAL* 6.2 0.7 - - + -
28C ASN 3.3 13.6 + - - +
29C ASN* 3.2 8.4 + - - +
30C LEU 3.2 0.6 - - - -
31C GLN* 1.3 76.6 - - + +
33C ALA* 1.3 61.9 + - - +
35C ILE* 3.1 3.8 + - - +
36C LYS* 2.9 45.0 + - + +
135C PRO* 3.8 32.5 - - + +
138C ILE* 4.0 17.0 - - + +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASN 3.0 13.4 + - - +
30C LEU 3.6 6.7 - - - +
32C VAL* 1.3 74.3 - - - +
34C PHE* 1.3 66.7 + - - +
36C LYS* 4.3 1.3 - - - +
37C VAL* 3.1 35.1 + - + +
125C PHE* 5.3 1.3 - - + -
129C VAL* 3.9 24.7 - - + -
138C ILE* 3.9 16.8 - - + +
143C ILE* 5.1 1.3 - - + -
172C PHE* 4.0 16.6 - - + -
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Residues in contact with PHE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU 2.8 17.2 + - - +
31C GLN* 3.6 9.0 - - - +
32C VAL 3.2 0.2 - - - -
33C ALA* 1.3 78.0 - - - +
35C ILE* 1.3 79.2 + - + +
37C VAL* 4.1 2.5 - - - +
38C ASP* 3.7 1.7 - - - +
56C ASP* 3.4 25.1 - - - -
59C ASN* 3.4 41.3 - - + -
60C ARG* 4.4 3.8 - - + -
63C PHE* 3.7 25.6 - + - -
169C LYS* 3.2 56.4 - - + +
172C PHE* 4.2 14.3 - - + -
173C ALA* 3.8 19.7 - - + -
176C ILE* 4.9 5.2 - - + -
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 3.4 45.8 - - + +
78A ILE* 3.8 13.0 - - + -
79A LYS* 3.7 48.0 + - + +
31C GLN 3.5 14.3 + - - +
32C VAL 3.1 6.3 + - - +
33C ALA 3.1 0.4 - - - -
34C PHE* 1.3 100.5 - - + +
36C LYS* 1.3 62.3 + - - +
37C VAL 3.4 0.5 + - - -
38C ASP* 3.5 19.1 + - - +
39C ASN* 4.8 0.9 + - - +
56C ASP* 4.4 8.5 - - - +
60C ARG* 4.8 2.7 - - - -
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 2.7 36.5 + - + +
79A LYS* 4.2 8.5 + - - +
81A PRO* 3.8 21.6 - - - +
32C VAL* 2.9 32.3 + - + +
33C ALA 3.2 0.6 + - - +
35C ILE* 1.3 71.2 - - - +
37C VAL* 1.3 66.6 + - - +
38C ASP 3.2 0.6 + - - -
39C ASN* 3.6 13.7 + - - +
40C VAL* 3.6 13.3 + - - +
138C ILE* 3.5 27.1 - - + +
139C ASN* 4.3 16.2 - - - +
140C THR* 5.2 7.0 + - - +
143C ILE* 3.8 19.7 - - + -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA* 3.1 23.3 + - - +
34C PHE 4.1 3.4 - - - +
35C ILE 3.3 0.2 - - - -
36C LYS* 1.3 76.4 - - - +
38C ASP* 1.3 75.8 + - - +
40C VAL* 2.8 20.3 + - - +
41C VAL* 2.9 23.1 + - + +
52C VAL* 5.0 0.2 - - + -
125C PHE* 4.1 17.0 - - + -
143C ILE* 4.4 7.8 - - + +
165C LEU* 3.9 43.0 - - + +
169C LYS* 4.1 14.1 - - + -
172C PHE* 4.8 5.6 - - + -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS* 3.8 21.5 + - - +
34C PHE 3.7 2.0 - - - +
35C ILE* 3.5 9.5 + - - +
36C LYS 3.2 1.8 - - - -
37C VAL* 1.3 75.8 - - - +
39C ASN* 1.3 65.0 + - - +
41C VAL* 3.3 4.9 + - - +
42C ALA* 3.3 17.5 + - - +
52C VAL* 3.7 24.2 - - + +
53C ASP* 4.2 12.7 - - - +
56C ASP* 3.2 22.4 - - - +
169C LYS* 2.8 45.6 + - - +
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS* 3.6 45.2 + - - +
80A ASN* 5.1 2.9 + - - +
35C ILE 4.8 0.6 + - - +
36C LYS* 3.6 9.2 + - - +
37C VAL 3.2 0.2 - - - -
38C ASP* 1.3 75.4 - - - +
40C VAL* 1.3 61.0 + - - +
42C ALA* 3.5 10.1 + - - +
43C SER* 3.0 25.5 + - - -
49C LYS* 5.4 8.5 - - - +
53C ASP* 5.2 3.8 + - - -
140C THR* 5.2 13.4 - - + +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS 3.6 14.8 - - - +
37C VAL* 2.8 7.9 + - - +
39C ASN* 1.3 76.7 - - + +
41C VAL* 1.3 65.3 + - - +
43C SER* 2.6 22.2 + - - -
44C PHE* 3.0 26.9 + - + -
140C THR* 4.1 26.5 - - + +
143C ILE* 4.0 28.9 - - + -
144C ARG* 3.7 10.8 - - + +
165C LEU* 3.4 26.0 - - + -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 2.9 17.6 + - + +
38C ASP 3.3 8.5 + - - +
40C VAL* 1.3 75.4 - - - +
42C ALA* 1.3 56.5 + - - +
44C PHE 3.3 0.5 + - - -
45C ASP 2.9 27.0 + - - +
48C GLN* 3.5 27.8 - - + +
52C VAL* 4.1 21.3 - - + -
162C ALA* 3.5 27.9 - - + +
165C LEU* 3.5 31.9 - - + -
166C LYS* 3.7 14.1 - - + +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP 3.3 9.2 + - - +
39C ASN* 3.6 15.7 - - - +
40C VAL 3.1 0.6 - - - -
41C VAL* 1.3 78.4 - - - +
43C SER* 1.3 65.4 + - - +
45C ASP 4.0 7.9 - - - -
46C PRO* 3.2 26.6 - - + +
49C LYS* 3.9 34.3 - - + -
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Residues in contact with SER 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN 3.0 13.6 + - - -
40C VAL* 2.6 25.7 + - - -
42C ALA* 1.3 76.5 - - - +
44C PHE* 1.3 63.6 + - - +
46C PRO* 4.2 5.4 - - - +
140C THR* 5.2 4.0 - - - +
144C ARG* 3.6 35.9 + - - -
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Residues in contact with PHE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.0 37.4 + - + -
41C VAL 3.8 5.2 - - - +
43C SER* 1.3 84.3 + - - +
45C ASP* 1.3 61.4 + - - +
46C PRO* 4.0 2.0 - - - +
144C ARG* 3.3 43.7 - - - -
147C MSE 4.0 18.2 - - + -
148C GLU* 3.8 17.3 - - - -
158C ASP* 3.6 52.8 - - - +
159C LYS* 4.3 2.1 + - - +
161C LYS* 3.7 28.7 - - + -
162C ALA* 4.1 5.4 - - + -
165C LEU* 4.4 6.5 - - + -
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL 2.9 12.4 + - - +
42C ALA* 3.5 3.7 - - - +
44C PHE* 1.3 78.0 - - - +
46C PRO* 1.3 58.6 - - - +
47C ASP* 3.2 20.5 + - - +
48C GLN* 2.8 52.4 + - + +
49C LYS 3.8 1.7 + - - -
159C LYS* 3.3 46.1 + - + +
162C ALA* 3.6 18.6 - - + -
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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
------------------------------------------------------------
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