Contacts of the helix formed by residues 28 - 37 (chain A) in PDB entry 1LT8
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 GLY 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY* 1.3 68.8 - - - -
29A PHE* 1.3 60.3 + - - -
30A VAL* 3.7 1.6 - - - -
31A PHE* 3.8 4.7 + - - +
32A ALA* 3.0 31.9 + - - +
63A PHE* 4.1 1.3 - - - -
299A CYS 3.4 25.9 + - - -
300A CYS* 4.1 5.6 - - - -
301A GLY 4.8 0.6 + - - -
302A PHE 3.2 14.7 + - - +
601A CBH 3.5 8.7 - - - -
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Residues in contact with PHE 29 (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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26A ASP* 3.6 19.1 - - - -
27A GLY 4.1 7.2 - - - -
28A GLY* 1.3 70.4 - - - +
30A VAL* 1.3 56.7 + - - +
33A LEU* 2.6 49.0 + - + +
56A VAL* 4.2 6.5 - - + -
59A LEU* 3.4 30.5 - - + -
60A HIS* 3.1 48.2 - + - -
63A PHE* 3.4 32.3 - + - -
72A GLN* 5.0 3.8 - - + -
74A PHE* 3.6 32.5 - + + -
601A CBH 2.9 17.2 + - - +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 5.3 0.2 - - - -
29A PHE* 1.3 74.6 - - - +
31A PHE* 1.3 76.8 + - + +
34A GLU* 2.8 31.8 + - - +
39A VAL* 3.8 10.5 - - + +
44A TRP* 3.8 40.4 - - + +
45A THR 5.5 0.2 - - - -
74A PHE* 3.7 23.1 - - + -
76A PHE* 4.0 16.4 - - + +
300A CYS* 4.7 1.3 - - - -
601A CBH 3.1 35.8 + - + +
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 3.8 3.8 + - - +
29A PHE 3.3 0.6 - - - -
30A VAL* 1.3 83.2 - - + +
32A ALA* 1.3 66.9 + - - +
34A GLU* 3.4 7.0 + - - +
35A LYS* 3.2 41.5 + - - +
44A TRP* 3.5 35.9 - + - -
251A TYR* 3.2 37.9 - + - -
261A PHE* 4.1 7.4 - + - -
267A PHE* 3.8 27.6 - + - -
268A PRO* 4.2 8.3 - - + -
271A LEU* 4.0 10.8 - - + -
300A CYS* 3.6 28.9 - - + -
301A GLY 4.1 13.2 - - - +
601A CBH 4.9 3.4 - - + -
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Residues in contact with ALA 32 (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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28A GLY 3.0 21.1 + - - +
29A PHE 3.7 2.5 - - - +
31A PHE* 1.3 76.8 - - - +
33A LEU* 1.3 64.2 + - - +
35A LYS* 3.3 6.3 + - - +
36A ARG* 3.3 29.6 + - - +
59A LEU* 4.0 22.9 - - + -
63A PHE* 5.2 1.3 - - + -
302A PHE 4.9 3.6 - - - +
303A GLU* 3.5 31.1 - - - +
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Residues in contact with LEU 33 (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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29A PHE* 2.6 31.3 + - + +
32A ALA* 1.3 70.2 - - - +
34A GLU* 1.3 66.0 + - - +
36A ARG* 3.0 9.6 + - - +
37A GLY 3.0 18.9 + - - -
38A TYR* 3.0 28.8 + - + -
39A VAL* 3.3 18.6 - - + +
48A ALA* 5.0 2.0 - - + -
55A ALA* 4.1 23.6 - - + +
56A VAL* 4.5 8.7 - - + -
59A LEU* 4.2 17.7 - - + -
74A PHE* 3.2 42.8 - - + -
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Residues in contact with GLU 34 (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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30A VAL 2.8 23.4 + - - +
31A PHE* 3.6 5.6 - - - +
33A LEU* 1.3 71.9 - - - +
35A LYS* 1.3 70.3 + - - +
37A GLY* 3.2 13.3 + - - -
39A VAL* 3.4 27.3 - - + +
41A ALA* 3.8 21.5 - - + +
44A TRP* 3.9 16.8 - - + -
269A PHE* 4.0 5.5 - - - -
278B ARG* 3.0 42.3 + - - -
308B ARG* 3.6 18.6 + - - -
327B LYS 4.4 1.6 - - - +
328B HIS* 4.2 5.0 - - - -
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Residues in contact with LYS 35 (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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31A PHE* 3.2 31.8 + - - +
32A ALA* 3.7 8.4 - - - +
33A LEU 3.2 0.2 - - - -
34A GLU* 1.3 89.3 - - - +
36A ARG* 1.3 60.2 + - + +
37A GLY 3.3 0.6 + - - -
251A TYR* 3.6 22.1 + - - -
272A GLU* 5.3 7.4 - - - -
301A GLY* 5.3 3.0 - - - -
303A GLU* 4.6 14.7 + - - +
278B ARG* 4.9 3.1 - - - +
303B GLU* 5.6 5.6 - - + +
304B PRO* 3.5 3.9 - - - +
305B TYR* 3.0 68.8 + - + +
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Residues in contact with ARG 36 (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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32A ALA* 3.3 17.7 + - - +
33A LEU* 3.0 13.8 + - + +
35A LYS* 1.3 78.5 - - + +
37A GLY* 1.3 57.8 + - - +
38A TYR* 3.5 21.3 - - + -
55A ALA 5.3 2.9 + - - -
58A GLN* 5.1 2.8 - - - +
59A LEU* 3.6 31.5 - - - +
62A GLU* 2.9 36.9 + - - -
303A GLU* 3.1 25.9 + - - -
304A PRO* 4.0 2.4 - - - +
36B ARG* 3.5 32.1 - - - +
62B GLU* 3.1 51.4 + - - +
65B ARG* 4.6 1.7 - - - -
303B GLU* 5.2 2.1 + - - +
304B PRO* 3.9 13.6 - - + +
324B ALA* 5.6 0.2 - - - +
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Residues in contact with GLY 37 (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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33A LEU 3.0 2.0 + - - -
34A GLU 3.2 10.7 + - - -
35A LYS 3.3 1.2 + - - -
36A ARG* 1.3 79.3 - - - +
38A TYR* 1.3 61.4 - - - +
39A VAL 3.7 1.1 - - - -
65B ARG* 2.7 32.7 + - - -
305B TYR* 6.5 0.2 - - - -
308B ARG* 3.9 15.7 - - - -
324B ALA* 4.2 10.2 - - - -
327B LYS* 3.6 10.1 - - - +
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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