Contacts of the helix formed by residues 24 - 37 (chain L) in PDB entry 1T6V
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18L ASP* 3.7 4.5 - - - -
19L ASN* 3.5 18.8 - - - -
22L GLY 3.7 4.4 + - - -
23L TYR* 1.3 75.9 - - - +
25L LEU* 1.3 64.2 + - - +
26L GLY 4.2 1.7 + - - -
27L ASN* 3.0 36.5 + - - +
28L TRP* 3.6 1.9 - - - -
120L VAL* 3.6 15.1 - - - +
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Residues in contact with LEU 25 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9L ALA 3.6 16.6 - - - +
12L MET* 3.7 19.5 - - + -
13L LYS* 3.6 42.6 - - + +
17L LEU* 4.7 2.9 - - + -
18L ASP* 2.9 36.5 + - + +
23L TYR 3.7 0.4 + - - -
24L SER* 1.3 71.8 - - - +
26L GLY* 1.3 62.3 + - - +
28L TRP* 3.1 21.8 + - + +
29L VAL* 3.2 13.5 + - + +
124L ILE* 4.1 28.7 - - + +
129L LEU* 4.2 13.2 - - + -
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Residues in contact with GLY 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L SER* 3.2 3.6 + - - -
25L LEU* 1.3 76.9 - - - +
27L ASN* 1.3 61.2 + - - +
29L VAL* 4.6 0.7 - - - -
30L CYS* 3.0 27.2 + - - +
120L VAL* 3.4 29.4 - - - -
121L GLN* 5.3 0.7 - - - -
123L TRP* 3.8 6.2 - - - +
124L ILE* 4.0 19.6 - - - +
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Residues in contact with ASN 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 4.0 10.8 - - + +
24L SER* 3.0 44.2 + - - +
26L GLY* 1.3 76.2 - - - +
28L TRP* 1.3 57.4 + - - +
30L CYS* 3.8 1.6 - - - +
31L ALA* 2.9 28.6 + - - +
105L MET* 3.7 21.3 - - - -
111L TRP* 2.8 33.8 + - - +
115L CYS 5.0 0.7 - - - +
116L LYS* 5.4 0.5 - - - -
120L VAL* 3.7 23.5 - - - +
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Residues in contact with TRP 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L MET* 3.5 28.8 - - + +
17L LEU* 3.2 58.2 + - + -
20L TYR* 4.2 7.3 + - + -
23L TYR* 3.2 19.4 + - + +
24L SER 3.6 14.8 - - - -
25L LEU* 3.1 10.2 + - - +
27L ASN* 1.3 75.2 - - + +
29L VAL* 1.3 59.8 + - - +
31L ALA* 3.4 4.0 + - - +
32L ALA 3.0 22.3 + - - -
56L LEU* 4.5 13.0 - - + +
95L ALA* 4.2 12.3 - - + -
99L VAL* 3.9 38.6 - - + -
105L MET* 3.8 26.2 - - + -
108L TRP* 3.9 26.5 - + - -
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Residues in contact with VAL 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ARG* 4.0 23.3 - - + +
8L LEU* 4.7 2.9 - - + -
9L ALA* 3.7 31.4 - - + +
12L MET* 4.0 15.0 - - - -
25L LEU* 3.2 16.4 + - + +
26L GLY 4.0 4.9 - - - +
27L ASN 3.4 0.2 - - - -
28L TRP* 1.3 75.6 - - - +
30L CYS* 1.3 59.0 + - - +
32L ALA* 3.2 3.2 + - - +
33L LYS* 2.9 24.9 + - - +
38L PHE* 3.6 18.6 - - + -
123L TRP* 3.9 25.8 - - + +
124L ILE* 4.4 6.7 - - + -
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Residues in contact with CYS 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L GLY 3.0 18.1 + - - +
27L ASN* 3.8 2.7 - - - +
29L VAL* 1.3 75.4 - - - +
31L ALA* 1.4 63.8 + - - +
33L LYS* 3.2 3.0 + - - -
34L PHE* 3.1 39.3 + - - +
114L ARG 4.0 2.7 - - - -
115L CYS* 2.0 51.1 - - + -
118L THR* 5.1 1.3 - - - -
120L VAL* 5.0 2.0 - - + -
123L TRP* 3.4 40.8 - - + +
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Residues in contact with ALA 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ASN 2.9 19.1 + - - +
28L TRP* 3.5 6.3 - - - +
30L CYS* 1.4 75.0 - - - +
32L ALA* 1.3 58.0 + - - +
34L PHE* 3.4 0.9 + - - +
35L GLU* 2.9 36.9 + - - +
56L LEU* 4.1 13.2 - - + -
105L MET* 3.8 19.5 - - + -
108L TRP* 4.8 7.2 - - + -
111L TRP* 4.2 14.4 - - + +
115L CYS* 3.6 7.5 - - - -
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Residues in contact with ALA 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LEU* 3.6 30.7 - - + -
12L MET* 4.1 5.8 - - + -
28L TRP 3.0 15.7 + - - +
29L VAL 3.2 1.3 + - - +
31L ALA* 1.3 72.4 - - - +
33L LYS* 1.3 67.5 + - - +
36L SER* 2.9 27.6 + - - -
37L ASN 3.2 1.6 + - - -
38L PHE* 3.6 3.3 + - + -
55L ILE* 3.7 28.3 - - + +
56L LEU* 4.1 3.5 - - + +
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Residues in contact with LYS 33 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29L VAL 2.9 12.8 + - - +
30L CYS 3.2 9.4 + - - +
32L ALA* 1.3 77.1 - - - +
34L PHE* 1.3 78.8 + - + +
37L ASN* 2.9 53.1 + - - +
38L PHE* 3.6 35.4 - - + -
123L TRP* 3.7 27.6 - - + -
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Residues in contact with PHE 34 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30L CYS* 3.1 30.6 + - - +
33L LYS* 1.3 91.8 - - + +
35L GLU* 1.3 62.0 + - - +
110L ALA* 3.6 30.8 - - + +
114L ARG* 3.4 65.5 - - + -
115L CYS* 4.1 0.7 - - - -
123L TRP* 3.5 39.9 - + - -
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Residues in contact with GLU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L ALA* 2.9 23.0 + - - +
32L ALA 4.1 0.9 - - - +
34L PHE* 1.3 79.7 - - - +
36L SER* 1.3 60.0 + - - +
37L ASN 3.8 0.2 - - - -
44L ASN* 4.8 4.2 + - - -
55L ILE 4.2 8.5 - - - +
56L LEU* 4.6 2.0 - - + -
57L GLN* 3.2 46.1 - - + +
108L TRP* 3.5 29.9 - - + -
109L VAL* 3.3 12.3 + - - +
110L ALA* 3.1 33.7 + - + -
100N ARG* 5.8 2.7 + - - -
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Residues in contact with SER 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ALA 2.9 11.1 + - - -
35L GLU* 1.3 74.9 - - - +
37L ASN* 1.3 70.9 - - - +
38L PHE 3.2 7.1 + - - -
39L ASN* 3.1 36.3 + - - +
42L ALA* 3.9 12.9 - - - +
54L GLY 3.6 12.6 - - - -
55L ILE* 2.8 33.0 + - - +
57L GLN* 4.6 0.2 - - - -
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Residues in contact with ASN 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L VAL* 4.2 10.0 - - - +
32L ALA 3.2 0.2 + - - -
33L LYS* 2.9 52.6 + - - +
34L PHE 4.8 0.2 - - - -
35L GLU 3.8 0.4 - - - -
36L SER* 1.3 79.0 - - - +
38L PHE* 1.3 72.1 + - - +
39L ASN* 3.3 3.0 + - + +
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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