Contacts of the helix formed by residues 24 - 40 (chain C) in PDB entry 4I5L
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 24 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLN* 5.4 0.4 - - - +
22C GLN* 5.7 0.4 - - - +
23C LEU* 1.3 78.0 - - - +
25C GLU* 1.3 59.8 + - - +
26C SER* 3.5 9.3 + - - -
27C GLN* 3.1 33.2 + - - +
28C VAL* 2.9 27.5 + - - +
137C TYR* 3.9 4.3 - - - -
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Residues in contact with GLU 25 (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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24C SER* 1.3 73.5 - - - +
26C SER* 1.3 59.5 + - - +
28C VAL* 3.3 2.9 + - - +
29C LYS* 2.9 28.1 + - - +
137C TYR* 3.6 17.3 - - + +
139C ASN* 3.0 25.6 + - - +
141C ASN* 2.9 32.0 + - + +
142C VAL* 4.0 26.0 - - + -
145C TYR* 4.1 14.9 + - + -
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER* 3.3 10.1 + - - -
25C GLU* 1.3 79.8 - - - +
27C GLN* 1.3 61.5 + - - +
29C LYS* 3.3 10.1 + - - +
30C SER* 3.0 29.5 + - - -
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 4.9 3.2 + - - +
12C GLN* 4.4 7.9 - - - +
13C TRP* 3.2 49.1 - - + +
16C GLN* 4.8 4.8 + - - +
23C LEU* 3.5 22.0 - - + +
24C SER* 3.1 35.3 + - - +
26C SER* 1.3 76.6 + - - +
28C VAL* 1.3 59.3 + - - +
30C SER* 3.4 2.9 + - - -
31C LEU* 2.8 32.7 + - - +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.1 13.5 - - + +
24C SER 2.9 20.5 + - - +
25C GLU 3.6 4.3 - - - +
27C GLN* 1.3 75.9 - - - +
29C LYS* 1.3 57.3 + - - +
31C LEU* 3.3 6.7 + - + +
32C CYS* 2.9 36.7 + - - -
98C THR* 4.6 7.6 - - + +
137C TYR* 3.8 21.5 - - + +
142C VAL* 4.1 15.5 - - + -
145C TYR* 4.4 8.1 - - + -
146C PHE* 3.6 40.8 - - + -
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Residues in contact with LYS 29 (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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25C GLU 2.9 16.7 + - - +
26C SER* 3.6 9.9 - - - +
27C GLN 3.3 0.2 - - - -
28C VAL* 1.3 75.5 - - - +
30C SER* 1.3 62.9 + - - +
32C CYS* 3.4 2.4 + - - +
33C GLU* 3.1 38.3 + - + +
145C TYR* 3.6 52.0 - - + +
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Residues in contact with SER 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 4.9 0.5 - - - -
13C TRP* 4.2 11.9 - - - -
26C SER 3.0 16.7 + - - -
27C GLN* 3.7 6.1 - - - -
29C LYS* 1.3 75.6 - - - +
31C LEU* 1.3 66.6 + - - +
32C CYS 3.2 0.3 + - - -
33C GLU* 3.2 7.5 + - - +
34C LYS* 3.1 46.2 + - - +
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Residues in contact with LEU 31 (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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6C PHE* 5.6 0.4 - - + -
10C LEU* 4.0 17.9 - - + -
13C TRP* 3.9 14.2 - - + -
23C LEU* 4.5 4.3 - - + -
27C GLN 2.8 21.5 + - - +
28C VAL* 3.6 6.5 - - - +
30C SER* 1.3 73.3 + - - +
32C CYS* 1.3 57.3 + - - +
34C LYS* 3.5 7.0 + - - +
35C ALA* 3.0 25.5 + - - +
98C THR* 3.8 34.1 - - + +
101C VAL* 3.3 26.2 - - + -
102C ALA* 3.8 23.6 - - + +
105C VAL* 3.9 16.8 - - + +
146C PHE* 5.3 3.8 - - + -
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Residues in contact with CYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 2.9 21.9 + - - +
29C LYS 3.9 3.6 - - - +
31C LEU* 1.3 76.5 - - - +
33C GLU* 1.3 65.1 + - - +
35C ALA* 3.2 6.5 + - - +
36C LYS* 2.9 33.8 + - - +
101C VAL* 5.2 1.8 - - - -
145C TYR* 3.9 35.2 - - + +
146C PHE* 3.9 30.7 - - - -
149C LEU* 3.9 15.3 - - + +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 3.1 31.9 + - + +
30C SER* 3.2 9.4 + - - +
32C CYS* 1.3 75.7 - - - +
34C LYS* 1.3 63.5 + - + +
36C LYS* 2.9 39.1 + - - +
37C GLU* 3.2 21.5 + - - +
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Residues in contact with LYS 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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6C PHE* 3.2 53.4 - - + -
30C SER* 3.1 31.3 + - - +
31C LEU* 3.8 8.3 - - - +
33C GLU* 1.3 76.2 - - + +
35C ALA* 1.3 61.3 + - - +
37C GLU* 3.5 6.9 + - - +
38C ILE* 3.3 29.9 + - + +
105C VAL* 4.2 13.2 - - + -
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Residues in contact with ALA 35 (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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31C LEU 3.0 18.0 + - - +
32C CYS 3.2 1.7 + - - +
34C LYS* 1.3 73.9 - - - +
36C LYS* 1.3 55.6 + - - +
38C ILE* 3.2 5.5 + - - +
39C LEU* 2.7 43.5 + - + +
101C VAL* 4.5 8.3 - - + -
104C LYS* 5.7 4.3 - - + -
105C VAL* 3.7 19.0 - - + +
149C LEU* 3.7 27.4 - - + -
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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
----------------------------------------------------------
32C CYS* 2.9 25.3 + - - +
33C GLU* 2.9 36.0 + - - +
35C ALA* 1.3 76.3 - - - +
37C GLU* 1.3 56.7 + - - +
39C LEU* 4.7 0.4 - - - -
40C THR* 2.9 36.0 + - - -
145C TYR 5.6 0.7 - - - -
148C ASP* 4.5 16.9 + - - +
149C LEU* 3.5 26.0 - - + +
152C TYR* 3.5 44.4 + - + +
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Residues in contact with GLU 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 GLU 3.2 10.4 + - - +
34C LYS* 3.7 11.7 - - - +
35C ALA 3.2 0.4 - - - -
36C LYS* 1.3 78.5 - - - +
38C ILE* 1.3 62.4 + - + +
40C THR* 3.2 24.8 - - - +
41C LYS* 4.0 9.2 - - - +
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Residues in contact with ILE 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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34C LYS* 3.3 17.2 + - + +
35C ALA* 3.2 7.0 + - - +
37C GLU* 1.3 77.2 - - + +
39C LEU* 1.3 64.0 + - + +
41C LYS* 3.2 19.9 + - - +
42C GLU* 3.9 10.5 + - - +
104C LYS* 4.2 22.2 - - + +
105C VAL* 3.9 36.6 - - + +
108C ARG* 3.6 63.5 - - + +
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Residues in contact with LEU 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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35C ALA* 2.7 24.1 + - + +
38C ILE* 1.3 74.2 - - + +
40C THR* 1.3 57.1 + - - +
42C GLU* 2.9 41.1 + - - +
104C LYS* 4.0 24.7 - - + -
113C ILE* 4.7 7.6 - - + +
149C LEU* 3.7 28.9 - - + -
152C TYR* 3.5 26.0 - - + +
153C LEU* 3.8 25.6 - - + +
154C PRO* 4.0 11.9 - - + -
185C ARG* 3.3 17.0 + - - -
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Residues in contact with THR 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 2.9 14.5 + - - +
37C GLU* 3.2 32.3 - - - +
39C LEU* 1.3 78.6 - - - +
41C LYS* 1.3 65.1 + - + +
42C GLU 3.6 4.2 + - - +
152C TYR* 3.9 24.0 - - - -
185C ARG* 4.9 3.5 + - - +
186C LEU* 4.7 9.4 - - - +
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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