Contacts of the helix formed by residues 26 - 34 (chain B) in PDB entry 1T4P
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 LYS 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLY 5.9 0.2 - - - -
23B GLY* 2.8 12.8 + - - +
25B GLU* 1.3 95.5 + - + +
27B GLY* 1.3 62.5 + - - +
28B PRO* 3.5 0.9 - - - -
29B ALA* 3.4 12.0 + - + +
30B ALA* 3.1 22.5 + - - +
280B PRO* 4.1 14.8 - - + -
281B THR* 3.9 29.1 - - + +
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY 3.9 0.8 + - - -
24B VAL 2.8 15.4 + - - -
26B LYS* 1.3 77.6 - - - +
28B PRO* 1.3 66.6 - - - +
30B ALA* 3.1 5.9 + - - +
31B LEU* 3.1 28.5 + - - +
98B GLY 3.8 5.8 - - - -
278B VAL* 3.5 21.0 + - - +
280B PRO* 4.2 5.2 - - - -
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Residues in contact with PRO 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA 4.0 9.4 - - - +
14B PRO* 4.0 8.7 - - + -
25B GLU 3.7 13.7 - - - +
26B LYS 3.8 0.2 - - - -
27B GLY* 1.3 90.3 - - - +
29B ALA* 1.3 61.2 + - - +
31B LEU* 3.4 3.3 + - + +
32B ARG* 3.1 35.7 + - - +
52B ASP* 3.5 23.6 - - - +
97B LEU* 3.3 43.5 - - + +
98B GLY 3.6 8.7 - - - +
99B GLY 3.8 4.5 - - - +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLU 5.2 0.6 + - - +
26B LYS* 3.4 14.9 + - + +
27B GLY 3.2 0.6 - - - -
28B PRO* 1.3 78.3 - - - +
30B ALA* 1.3 57.8 + - - +
32B ARG* 3.2 9.4 + - - +
33B LYS* 2.8 32.4 + - - +
52B ASP* 5.0 4.4 + - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS 3.1 3.6 + - - +
27B GLY* 3.5 8.5 - - - +
29B ALA* 1.3 79.5 - - - +
31B LEU* 1.3 57.1 + - - +
33B LYS* 3.2 8.7 + - - +
34B ALA* 3.0 29.3 + - - +
278B VAL* 5.0 1.1 - - + -
280B PRO* 3.6 30.1 - - + -
289B VAL* 5.8 0.9 - - + -
293B VAL* 3.6 21.1 - - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY 3.1 24.2 + - - +
28B PRO 3.9 3.8 - - - +
30B ALA* 1.3 75.5 - - - +
32B ARG* 1.3 59.1 + - - +
34B ALA* 3.6 7.6 + - - +
35B GLY 3.7 0.2 + - - -
36B LEU* 3.0 41.7 + - + +
97B LEU* 3.2 32.1 - - + -
98B GLY 5.1 1.3 - - - +
275B ILE* 4.2 16.2 - - + +
278B VAL* 4.6 15.5 - - + -
293B VAL* 3.9 20.9 - - + +
296B ALA* 3.6 30.7 - - + -
297B VAL* 4.0 10.8 - - + +
300B THR* 6.0 0.4 - - - +
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.8 16.9 - - - +
12B GLY* 3.8 4.4 - - - +
28B PRO* 3.1 34.0 + - - +
29B ALA* 3.7 6.1 - - - +
31B LEU* 1.3 73.2 - - - +
33B LYS* 1.3 59.4 + - - +
34B ALA 3.0 1.8 - - - -
35B GLY* 2.8 24.9 + - - -
36B LEU* 3.9 6.0 + - + +
37B VAL* 4.4 13.6 - - + +
38B GLU* 4.4 5.0 - - - +
49B ASP* 2.8 40.6 + - - -
51B GLY* 3.6 18.7 + - - -
52B ASP* 3.1 39.6 + - - -
97B LEU* 4.6 8.7 - - + -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA 2.8 18.2 + - - +
30B ALA* 3.5 9.0 - - - +
32B ARG* 1.3 76.1 - - - +
34B ALA* 1.3 55.6 + - - +
35B GLY* 3.1 3.5 + - - -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ALA 3.0 6.4 + - - +
31B LEU 3.8 6.1 - - - +
32B ARG 3.0 0.8 - - - -
33B LYS* 1.3 76.2 - - - +
35B GLY* 1.3 60.4 + - - +
36B LEU 3.5 0.9 - - - -
39B LYS* 3.5 19.4 - - - +
293B VAL* 3.4 32.5 - - + -
294B ASN* 4.5 10.7 - - - +
297B VAL* 4.1 9.3 - - + +
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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
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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