Contacts of the helix formed by residues 31 - 42 (chain M) in PDB entry 1T4F
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 31 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29M ARG 3.8 0.6 + - - +
30M PRO* 1.3 74.8 - - - +
32M PRO* 1.3 80.0 - - + +
33M LEU* 3.4 3.8 - - + +
34M LEU 3.0 4.8 + - - +
35M LEU* 2.9 19.3 + - - +
85M LEU* 6.2 0.2 - - + -
105M ARG 3.2 17.6 + - - +
106M ASN* 3.0 49.1 + - + +
107M LEU* 3.7 9.2 - - - +
108M VAL* 5.5 5.8 - - + -
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Residues in contact with PRO 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M PRO 4.6 0.4 - - - +
31M LYS* 1.3 88.5 - - + -
33M LEU* 1.3 65.1 + - + +
35M LEU* 3.2 12.7 + - + +
36M LYS* 3.0 26.0 + - - +
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Residues in contact with LEU 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M LYS* 3.4 2.1 - - + +
32M PRO* 1.3 83.1 - - + +
34M LEU* 1.3 65.7 + - - +
36M LYS* 3.3 22.6 + - - +
37M LEU* 3.1 19.9 + - - +
81M LEU* 3.8 32.0 - - + +
84M ASP* 4.7 12.6 - - + +
85M LEU* 3.3 23.9 - - + +
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Residues in contact with LEU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M PRO* 3.6 19.3 - - + -
31M LYS* 3.0 9.7 + - + +
33M LEU* 1.3 75.0 - - - +
35M LEU* 1.3 60.9 + - - +
37M LEU* 3.1 19.6 + - + +
38M LEU* 2.8 46.8 + - + +
53M VAL* 4.6 15.0 - - + -
57M LEU* 6.2 3.8 - - + -
85M LEU* 3.8 17.0 - - + +
86M PHE* 6.4 2.2 - - + -
103M ILE* 4.7 4.3 - - + +
106M ASN* 3.3 41.7 - - + +
107M LEU* 4.3 14.8 - - + -
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Residues in contact with LEU 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M PRO* 4.0 24.8 - - + +
31M LYS 2.9 12.2 + - - +
32M PRO* 3.3 14.6 - - + +
34M LEU* 1.3 78.3 - - - +
36M LYS* 1.3 57.3 + - - +
38M LEU* 3.2 2.5 + - - +
39M LYS* 2.8 54.2 + - + +
44M GLN* 4.3 20.4 - - + +
45M LYS 5.2 2.9 - - - +
48M TYR* 4.0 17.7 - - + +
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Residues in contact with LYS 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M PRO 3.0 12.5 + - - +
33M LEU* 3.4 25.6 - - - +
34M LEU 3.2 0.2 - - - -
35M LEU* 1.3 77.3 - - - +
37M LEU* 1.3 64.1 + - - +
39M LYS* 3.4 9.4 + - - +
40M SER* 3.2 20.0 + - - -
81M LEU* 4.1 20.3 - - + +
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Residues in contact with LEU 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M LEU 3.1 11.9 + - - +
34M LEU* 3.1 23.5 + - + +
36M LYS* 1.3 76.0 - - - +
38M LEU* 1.3 75.6 + - + +
40M SER* 2.7 27.2 + - - -
41M VAL* 3.9 3.5 + - + +
56M TYR 4.9 1.1 - - - +
57M LEU* 4.6 14.8 - - + -
60M TYR* 3.2 62.3 - - + +
81M LEU* 4.1 15.4 - - + +
82M LEU* 4.7 9.6 - - + +
85M LEU* 4.3 11.7 - - + -
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Residues in contact with LEU 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M PRO* 3.9 31.4 - - + -
34M LEU* 2.8 30.2 + - + +
35M LEU* 3.6 4.3 - - - +
37M LEU* 1.3 84.4 - - + +
39M LYS* 1.3 56.6 + - - +
41M VAL* 3.3 6.5 + - - +
42M GLY* 2.8 30.2 + - - -
43M ALA 4.9 1.3 - - - +
48M TYR* 4.2 29.6 - - + +
53M VAL* 4.3 29.4 - - + +
56M TYR* 3.6 33.2 - - + -
57M LEU* 4.8 1.6 - - + +
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Residues in contact with LYS 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M LEU* 2.8 49.9 + - + +
36M LYS* 3.8 8.1 - - - +
37M LEU 3.3 0.2 - - - -
38M LEU* 1.3 72.5 - - - +
40M SER* 1.3 61.5 + - - +
41M VAL 3.2 0.2 - - - -
42M GLY 3.3 17.6 - - - +
44M GLN* 3.4 44.4 - - + +
48M TYR* 4.8 0.4 - - - +
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Residues in contact with SER 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36M LYS* 3.2 11.2 + - - -
37M LEU 2.7 20.2 + - - -
39M LYS* 1.3 78.2 - - - +
41M VAL* 1.3 62.8 + - - +
60M TYR* 3.4 25.6 - - - -
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Residues in contact with VAL 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M LEU* 4.3 6.5 - - + +
38M LEU* 3.7 8.1 - - - +
39M LYS 4.5 0.2 - - - -
40M SER* 1.3 93.5 + - - +
42M GLY* 1.3 58.7 + - - +
56M TYR* 3.7 42.4 - - + +
59M GLN* 4.6 8.1 - - + -
60M TYR* 3.9 25.6 - - + +
63M THR* 4.1 16.2 - - + -
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Residues in contact with GLY 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M LEU 2.8 14.3 + - - +
39M LYS* 3.3 18.0 - - - +
41M VAL* 1.3 80.9 - - - +
43M ALA* 1.3 65.4 + - - -
44M GLN 4.1 0.5 + - - -
56M TYR* 3.4 21.3 - - - -
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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