Contacts of the helix formed by residues 31 - 45 (chain A) in PDB entry 5D4E
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 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 1.3 77.8 - - - +
32A PHE* 1.3 53.8 + - - -
33A GLY 3.3 0.7 - - - -
34A VAL* 3.8 2.2 + - - -
35A THR* 2.7 28.6 + - - -
193A ASP* 2.6 15.3 + - - -
42B ARG* 2.9 27.6 + - - -
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Residues in contact with PHE 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 LEU* 4.1 19.1 - - + +
29A GLU* 3.1 37.8 + - + +
30A ARG 4.0 7.0 - - - -
31A GLY* 1.3 77.6 - - - +
33A GLY* 1.3 61.2 + - - +
34A VAL 3.2 1.6 - - - -
35A THR* 3.6 16.4 - - + -
36A LEU* 2.9 34.9 + - + +
193A ASP* 2.9 1.6 + - - -
43B ILE* 4.1 22.0 - - + -
46B SER* 4.7 4.7 - - - -
47B SER* 3.0 29.2 - - - -
217B ILE* 3.9 18.6 - - + -
218B LEU* 5.8 0.2 - - + -
221B HIS* 3.5 40.2 - + + +
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.8 0.4 - - - -
32A PHE* 1.3 77.0 - - - +
34A VAL* 1.3 56.6 + - - +
37A GLY* 2.9 26.3 + - - -
179A PHE* 3.8 1.6 - - - -
181A VAL* 3.7 22.7 - - - -
193A ASP* 2.9 23.9 + - - +
195A LEU* 3.4 22.0 - - - +
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Residues in contact with VAL 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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31A GLY* 3.8 2.3 + - - -
32A PHE 3.2 0.2 - - - -
33A GLY* 1.3 76.2 - - - +
35A THR* 1.3 66.2 + - - +
38A ASN* 2.9 22.8 + - + +
39A PRO* 3.5 3.6 - - - +
179A PHE* 4.0 9.9 - - + -
181A VAL* 4.6 3.8 - - + +
193A ASP* 4.8 0.4 + - - -
42B ARG* 3.5 38.8 - - - +
939C ARG* 4.1 28.0 - - + +
979C THR 3.5 23.3 - - - +
980C GLY* 4.1 18.4 - - - +
981C GLU* 4.3 2.0 - - - +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 2.7 23.8 + - - -
32A PHE* 3.4 20.1 + - + -
34A VAL* 1.3 77.6 - - - +
36A LEU* 1.3 58.8 + - + +
39A PRO* 3.1 24.4 - - - +
218A LEU* 6.0 0.2 - - - +
39B PRO* 3.8 26.8 - - + +
42B ARG* 2.9 25.1 + - - +
43B ILE* 3.8 28.6 - - + +
218B LEU* 4.5 7.0 - - + +
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Residues in contact with LEU 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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25A LEU* 3.9 22.7 - - + -
28A LEU* 4.2 9.0 - - + -
32A PHE* 2.9 17.9 + - + +
35A THR* 1.3 77.8 - - - +
37A GLY* 1.3 67.6 + - - +
38A ASN 3.5 0.2 - - - -
39A PRO* 3.4 7.3 - - - +
40A LEU* 3.3 26.9 - - + +
195A LEU* 3.9 10.5 - - + -
218A LEU* 5.6 1.7 - - + +
218B LEU* 4.0 19.7 - - + -
221B HIS* 3.7 55.2 - - + +
222B LEU* 4.2 20.0 - - + -
225B PHE* 5.0 4.5 - - + -
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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 GLY 2.9 21.6 + - - -
34A VAL 3.2 0.2 + - - -
36A LEU* 1.3 79.3 - - - +
38A ASN* 1.3 62.4 + - - +
40A LEU* 3.5 4.7 + - - +
41A ARG* 3.3 19.1 + - - +
179A PHE* 3.9 19.7 - - - -
195A LEU* 3.7 14.1 - - - +
197A LEU* 4.1 7.0 - - - +
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Residues in contact with ASN 38 (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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34A VAL 2.9 15.6 + - - +
37A GLY* 1.3 69.8 - - - +
39A PRO* 1.3 71.3 - - + +
41A ARG* 3.0 9.8 + - - +
42A ARG* 3.0 32.4 + - - +
179A PHE* 3.5 24.2 - - + -
38B ASN* 6.0 1.2 - - - +
860C HIS* 4.7 3.6 + - - -
976C ASP 4.1 1.6 - - - +
977C GLY* 3.3 24.0 + - - +
978C ARG 3.7 4.6 + - - -
979C THR 3.0 34.6 + - - +
980C GLY* 3.3 14.1 + - - -
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Residues in contact with PRO 39 (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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34A VAL 3.5 4.0 - - - +
35A THR* 3.1 28.3 - - - +
36A LEU 3.4 6.3 - - - +
38A ASN* 1.3 95.0 - - + +
40A LEU* 1.3 61.0 + - - +
42A ARG* 3.3 7.0 + - + +
43A ILE* 3.1 30.8 + - - +
218A LEU* 4.2 18.8 - - + -
35B THR* 4.0 26.1 - - + +
39B PRO* 3.4 23.1 - - + -
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Residues in contact with LEU 40 (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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36A LEU* 3.3 19.2 + - + +
37A GLY 3.5 7.8 + - - +
38A ASN 3.2 0.6 - - - -
39A PRO* 1.3 76.2 - - - +
41A ARG* 1.3 58.1 + - - +
43A ILE* 3.8 4.3 - - + +
44A LEU* 2.9 42.5 + - + +
195A LEU* 5.7 0.2 - - + -
197A LEU* 3.7 29.6 - - + -
211A LEU* 3.8 9.6 - - + -
214A ALA* 4.6 6.7 - - + +
215A VAL* 4.2 25.6 - - + +
218A LEU* 4.1 23.1 - - + -
222B LEU* 4.4 4.9 - - + -
225B PHE* 3.8 27.1 - - + -
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Residues in contact with ARG 41 (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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37A GLY 3.3 9.6 + - - +
38A ASN* 3.0 13.7 + - - +
40A LEU* 1.3 79.1 - - - +
42A ARG* 1.3 63.1 + - + +
44A LEU* 3.3 1.1 + - - +
45A LEU* 3.0 48.9 + - + +
177A VAL* 3.0 47.5 + - + +
178A ALA* 4.8 0.6 - - - +
179A PHE* 4.3 21.8 - - + -
197A LEU* 5.2 0.4 - - - +
855C VAL 4.7 6.5 + - - -
856C GLU* 4.1 19.6 + - - +
858C MET 4.9 0.2 + - - -
860C HIS* 3.2 54.2 + - - +
864C GLY 3.5 14.8 + - - -
866C PRO* 4.8 4.8 - - - +
977C GLY* 4.1 5.3 + - - -
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Residues in contact with ARG 42 (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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38A ASN* 3.0 27.8 + - - +
39A PRO* 3.3 9.4 + - - +
41A ARG* 1.3 78.7 - - + +
43A ILE* 1.3 52.6 + - - +
45A LEU 3.7 0.2 + - - -
46A SER* 2.6 32.9 + - - -
31B GLY* 2.9 30.7 + - - -
34B VAL* 3.3 16.8 - - - +
35B THR* 2.8 34.3 + - - +
856C GLU* 3.1 45.7 + - + +
857C ASP* 3.3 21.8 + - - -
977C GLY 3.1 29.1 + - - +
978C ARG* 3.5 15.3 - - - +
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Residues in contact with ILE 43 (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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39A PRO 3.1 18.0 + - - +
40A LEU* 3.9 5.2 - - - +
42A ARG* 1.3 75.2 - - - +
44A LEU* 1.3 63.4 + - - +
45A LEU 3.2 0.2 - - - -
46A SER* 3.7 4.3 - - - -
47A SER* 2.9 30.6 + - - -
48A ILE* 3.6 6.1 + - + +
214A ALA* 3.8 20.6 - - + +
217A ILE* 3.8 39.5 - - + -
218A LEU* 3.6 45.5 - - + +
32B PHE* 4.0 16.2 - - + -
35B THR* 4.2 6.5 - - + -
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Residues in contact with LEU 44 (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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40A LEU* 2.9 36.1 + - + +
41A ARG 3.8 1.1 - - - +
43A ILE* 1.3 77.3 - - - +
45A LEU* 1.3 60.5 + - - +
48A ILE* 3.6 10.1 - - + +
172A SER* 4.0 2.9 + - - -
174A VAL* 3.2 29.3 - - + +
177A VAL* 3.7 26.5 - - + -
197A LEU* 5.2 3.8 - - + -
199A ILE* 3.6 27.6 - - + -
210A ALA* 3.4 47.3 - - + +
211A LEU* 3.8 9.0 - - + +
214A ALA* 3.8 9.6 - - + -
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Residues in contact with LEU 45 (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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41A ARG* 3.0 58.7 + - + +
42A ARG 4.3 3.6 - - - +
43A ILE 3.2 0.4 - - - -
44A LEU* 1.3 77.6 - - - +
46A SER* 1.3 58.8 + - - +
172A SER* 4.1 12.4 + - - -
174A VAL* 4.5 12.1 - - + +
175A ARG 4.8 3.6 - - - +
176A ARG* 4.6 5.4 - - - -
177A VAL* 4.0 29.4 - - + +
696C LYS* 5.0 5.4 + - - -
855C VAL* 3.9 41.2 - - + +
856C GLU* 4.4 11.8 - - + +
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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