Contacts of the helix formed by residues 30 - 43 (chain A) in PDB entry 6DVD
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 PHE 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.4 5.6 - - + -
27A GLU* 3.0 39.4 + - + +
28A PRO 3.2 1.6 - - - +
29A GLY* 1.3 76.7 - - - +
31A GLY* 1.3 64.0 + - - +
32A TYR 3.3 1.5 + - - -
33A THR* 3.5 6.6 + - - -
34A LEU* 3.3 47.8 + - + +
37B SER* 4.6 3.8 - - - -
40B ARG* 3.6 23.1 - - + -
41B THR* 3.1 51.1 - - + -
44B SER* 4.8 2.9 - - - -
45B SER* 4.4 9.6 - - - -
215B LEU* 4.1 5.8 - - + -
218B LEU* 3.7 17.0 - - + -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.1 19.5 - - - +
29A GLY 3.4 1.4 - - - -
30A PHE* 1.3 78.5 - - - +
32A TYR* 1.3 61.6 + - - +
34A LEU* 3.5 0.9 + - - -
35A GLY 3.3 17.3 + - - -
178A VAL* 3.6 17.7 - - - -
190A ASP* 4.0 16.0 + - - +
192A LEU* 3.4 16.3 - - - +
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Residues in contact with TYR 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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29A GLY* 4.4 8.1 + - - +
30A PHE 3.3 0.6 - - - -
31A GLY* 1.3 76.2 - - - +
33A THR* 1.3 62.1 + - - +
35A GLY 3.6 0.2 + - - -
36A ASN* 3.3 23.6 + - - +
176A TYR* 3.7 23.3 + + - -
177A LYS* 4.9 0.7 - - - -
178A VAL* 3.4 50.0 + - + +
190A ASP* 5.5 1.1 + - - -
1011C PHE* 3.7 24.3 - + - -
1016C GLY* 3.9 12.4 - - - +
1017C GLU* 4.0 20.4 - - - +
1018C PRO* 3.6 33.8 - - + +
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY 4.0 8.8 + - - -
30A PHE* 3.5 8.8 + - - -
31A GLY 3.3 0.2 - - - -
32A TYR* 1.3 74.1 - - - +
34A LEU* 1.3 64.1 + - - +
36A ASN* 4.0 1.0 - - - +
37A SER* 3.1 30.1 + - - +
33B THR 5.4 0.7 - - - +
36B ASN* 3.4 30.5 + - + +
37B SER* 3.3 35.6 + - - +
40B ARG* 4.3 11.3 - - - +
1015C SER 3.8 9.9 - - - +
1017C GLU* 3.4 19.1 + - - -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.9 4.0 - - + -
26A LEU* 3.6 26.7 - - + -
30A PHE* 3.3 34.8 + - + +
31A GLY 4.0 0.9 - - - +
32A TYR 3.3 0.4 - - - -
33A THR* 1.3 77.7 - - - +
35A GLY* 1.3 64.8 + - - +
37A SER* 3.3 3.7 + - - -
38A LEU* 3.1 29.9 + - + +
192A LEU* 3.8 15.7 - - + -
37B SER* 5.3 3.1 - - - +
215B LEU* 4.5 2.7 - - + -
218B LEU* 3.6 37.7 - - + -
219B PHE* 3.5 32.8 - - + -
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Residues in contact with GLY 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 GLY 3.3 8.3 + - - -
32A TYR 3.6 1.3 + - - -
34A LEU* 1.3 79.2 - - - +
36A ASN* 1.3 57.6 + - - +
38A LEU* 3.7 3.1 + - - +
39A ARG* 2.9 28.1 + - - +
176A TYR* 3.3 21.9 - - - -
192A LEU* 3.5 22.1 - - - +
194A LEU* 4.0 7.8 - - - +
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Residues in contact with ASN 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 TYR 3.3 7.2 + - - +
33A THR 4.0 2.0 - - - +
34A LEU 3.2 0.8 - - - -
35A GLY* 1.3 75.9 - - - +
37A SER* 1.3 58.0 + - - +
38A LEU 3.2 0.2 - - - -
39A ARG* 4.2 4.6 - - - +
40A ARG* 2.7 61.6 + - - +
176A TYR* 3.3 22.8 + - - +
32B TYR 5.2 0.3 - - - +
33B THR* 5.6 0.9 - - - +
906C PHE* 4.2 8.5 - - - -
1013C GLY* 3.3 25.5 + - - +
1014C ARG 3.7 1.6 - - - +
1015C SER 3.2 23.0 + - - +
1016C GLY* 3.5 17.2 - - - -
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 3.1 9.5 + - - +
34A LEU 3.3 4.2 + - - -
36A ASN* 1.3 78.4 + - - +
38A LEU* 1.3 60.4 + - - +
40A ARG* 4.3 0.7 - - - +
41A THR* 2.8 28.8 + - - -
215A LEU* 3.6 7.5 - - - +
219A PHE* 5.3 3.1 - - - -
33B THR* 2.7 30.3 + - - +
37B SER* 2.4 29.9 + - - -
219B PHE* 4.2 17.3 - - - -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.8 17.9 - - + -
34A LEU* 3.1 24.3 + - + +
35A GLY* 4.0 5.6 - - - +
37A SER* 1.3 74.5 - - - +
39A ARG* 1.3 59.6 + - - +
41A THR* 3.3 2.9 + - - -
42A LEU* 2.8 35.6 + - + +
192A LEU* 5.0 4.5 - - + -
194A LEU* 3.7 29.8 - - + -
208A LEU* 3.8 23.1 - - + -
211A ALA* 4.5 10.9 - - + +
215A LEU* 3.8 9.0 - - + -
219B PHE* 3.6 31.6 - - + -
222B ALA* 5.0 7.2 - - + -
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Residues in contact with ARG 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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35A GLY 2.9 20.5 + - - +
36A ASN* 3.1 10.1 + - - +
38A LEU* 1.3 76.4 - - - +
40A ARG* 1.3 57.1 + - - +
42A LEU* 3.6 0.6 - - - +
43A LEU* 2.9 54.8 + - + +
174A VAL* 3.1 47.5 + - + +
176A TYR* 3.9 8.1 - - + -
901C VAL 4.3 10.5 + - - -
902C GLU* 3.4 21.6 + - - +
906C PHE* 3.2 65.0 - - - +
910C GLY 3.4 14.6 + - - -
912C PRO* 4.4 4.2 - - - +
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Residues in contact with ARG 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 ASN* 2.7 41.5 + - - +
37A SER 4.3 1.3 - - - +
39A ARG* 1.3 73.0 - - - +
41A THR* 1.3 51.6 + - - +
43A LEU 3.8 1.0 + - - -
44A SER* 2.5 34.4 + - - -
29B GLY* 3.2 26.3 + - - -
32B TYR* 3.7 17.0 - - - +
33B THR* 3.2 37.9 - - + +
902C GLU* 3.4 35.7 + - + +
903C ASP* 2.6 32.3 + - - -
1013C GLY 2.3 44.2 + - - +
1014C ARG* 3.5 4.4 - - - +
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Residues in contact with THR 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 SER 2.8 19.2 + - - -
38A LEU 3.8 2.9 - - - -
39A ARG 3.3 0.6 - - - -
40A ARG* 1.3 76.2 - - - +
42A LEU* 1.3 64.8 + - - +
44A SER* 3.6 3.4 - - - -
45A SER* 3.1 25.3 + - - +
46A ILE* 3.8 4.0 - - - +
211A ALA* 3.8 19.7 - - + +
214A THR* 3.8 36.3 - - + +
215A LEU* 3.3 18.6 - - + +
30B PHE* 3.4 17.8 - - + -
33B THR* 4.8 1.6 - - - -
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Residues in contact with LEU 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 LEU 2.8 26.2 + - - +
39A ARG 3.6 3.8 - - - +
41A THR* 1.3 77.2 - - - +
43A LEU* 1.3 59.1 + - - +
44A SER 3.0 5.9 + - - -
46A ILE* 3.1 26.2 - - + +
169A SER* 3.8 2.3 + - - -
171A VAL* 3.2 15.7 - - + +
174A VAL* 3.9 26.5 - - + -
194A LEU* 4.4 8.7 - - + -
196A VAL* 3.7 31.0 - - + -
207A ALA* 3.4 41.1 - - + +
208A LEU* 3.8 6.7 - - + +
211A ALA* 3.8 13.2 - - + -
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Residues in contact with LEU 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 ARG* 2.9 64.5 + - + +
40A ARG 3.8 2.4 + - - +
41A THR 3.5 0.4 - - - -
42A LEU* 1.3 73.4 - - - +
44A SER* 1.3 57.0 + - - +
145A GLY* 6.0 0.2 - - - -
169A SER* 4.2 11.7 + - - -
171A VAL* 3.6 25.6 - - + +
172A LEU 4.8 3.6 - - - +
173A LYS* 4.8 5.2 - - - -
174A VAL* 4.0 18.8 - - + +
901C VAL* 4.4 21.7 - - + +
902C GLU* 4.2 24.5 - - + +
910C GLY 5.6 0.4 - - - +
912C PRO* 6.3 0.7 - - + -
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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