Contacts of the helix formed by residues 35 - 50 (chain D) in PDB entry 1DVM
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 SER 35 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D PHE* 1.3 78.8 - - - +
36D PRO* 1.4 58.9 - - - +
37D TYR* 4.7 0.9 - - - +
38D GLY* 2.9 17.7 + - - -
39D VAL* 3.0 25.1 + - - +
169D LEU* 3.2 39.5 - - - +
322D GLN* 3.1 17.3 + - - -
324D VAL* 4.0 1.8 - - - -
371D LEU 3.0 14.1 + - - -
372D PHE* 3.9 6.5 - - - -
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Residues in contact with PRO 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA 4.6 2.5 - - - -
13D SER* 4.1 6.3 - - - +
16D GLY* 3.7 33.8 - - - +
17D VAL 4.6 0.2 - - - +
34D PHE* 3.6 9.8 - - + +
35D SER* 1.4 81.8 - - - +
37D TYR* 1.3 64.1 + - - +
39D VAL* 3.3 7.0 - - + +
40D ALA* 3.1 23.6 + - - +
370D VAL* 3.4 29.8 - - + +
371D LEU 3.4 17.3 - - - +
372D PHE* 3.8 4.5 - - - -
373D MET* 3.8 21.3 - - + +
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Residues in contact with TYR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA* 5.0 14.6 + - + -
13D SER* 5.3 0.4 - - - +
35D SER* 4.8 2.7 - - - -
36D PRO* 1.3 79.3 - - - +
38D GLY* 1.3 63.6 + - - +
40D ALA* 3.4 5.3 + - - +
41D SER* 2.6 52.8 + - - -
75D LEU* 4.9 8.6 + - + -
78D LEU* 4.2 17.5 - - + -
79D TYR* 3.6 34.3 + + - +
82D LEU* 3.7 24.0 - - + +
83D MET* 6.3 0.9 - - + -
91D ILE* 5.7 4.0 - - + -
93D THR* 5.5 4.5 - - + -
169D LEU* 5.0 10.1 - - + -
369D THR* 3.6 22.7 - - + -
370D VAL 3.4 16.8 + - - +
371D LEU* 3.8 19.1 - - + +
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Residues in contact with GLY 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER* 2.9 23.7 + - - -
36D PRO 3.2 0.2 - - - -
37D TYR* 1.3 82.9 - - - +
39D VAL* 1.3 61.5 + - - +
41D SER* 3.3 11.9 + - - -
42D VAL* 3.4 13.0 + - - +
95D ASP* 5.1 0.4 - - - -
167D ASN* 3.1 27.0 - - - +
169D LEU* 4.2 8.3 - - - -
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Residues in contact with VAL 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 4.1 2.9 - - + -
16D GLY* 3.8 19.7 - - - -
19D VAL* 4.0 17.0 - - + -
34D PHE* 4.2 8.5 - - + -
35D SER 3.0 9.6 + - - +
36D PRO 3.3 11.9 - - - +
38D GLY* 1.3 74.3 - - - +
40D ALA* 1.3 66.6 + - - +
42D VAL* 3.1 19.5 - - - +
43D LEU* 3.1 25.3 + - + +
167D ASN* 4.1 0.4 - - - -
286D LEU* 3.6 43.7 - - + -
290D LEU* 5.0 1.3 - - + -
322D GLN* 3.5 14.4 - - - +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.4 42.4 - - + +
15D PHE* 3.8 21.3 - - + -
36D PRO 3.1 9.6 + - - +
37D TYR 3.9 3.6 - - - +
39D VAL* 1.3 78.6 - - - +
41D SER* 1.3 60.9 + - - +
44D ALA* 2.9 26.2 + - - +
62D MET* 3.1 15.4 - - + +
64D PHE* 5.2 1.0 - - + -
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Residues in contact with SER 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D TYR* 2.6 50.6 + - - -
38D GLY* 3.5 6.7 - - - -
39D VAL 3.3 0.2 - - - -
40D ALA* 1.3 72.7 - - - +
42D VAL* 1.3 66.5 + - - +
44D ALA* 3.1 16.8 + - - +
45D MET* 3.1 20.1 + - - +
75D LEU* 5.8 4.9 - - - +
95D ASP* 4.1 16.4 - - - -
117D PHE* 4.6 3.0 - - - -
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLY 3.4 7.4 - - - +
39D VAL* 3.1 20.0 - - + +
41D SER* 1.3 75.5 - - - +
43D LEU* 1.3 74.5 + - + +
45D MET* 3.0 13.5 + - - +
46D LEU* 2.8 28.6 + - - +
95D ASP* 3.4 33.7 - - + +
96D ALA 4.5 0.9 - - - +
165D LEU* 3.6 29.5 - - + +
166D VAL 3.6 9.0 - - - +
167D ASN* 3.6 23.3 - - + +
286D LEU* 5.2 0.2 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 4.2 15.0 - - + -
39D VAL* 3.1 36.9 + - + +
40D ALA 3.9 1.3 - - - +
42D VAL* 1.3 91.6 - - + +
44D ALA* 1.3 61.9 + - - +
46D LEU* 3.4 29.4 + - + +
47D GLN* 3.1 22.9 + - - +
58D ILE* 4.2 20.9 - - + +
62D MET* 3.7 18.3 - - + +
165D LEU* 5.0 4.9 - - + -
286D LEU* 4.9 3.4 - - + -
290D LEU* 4.2 28.7 - - + -
295D MET* 4.5 2.9 - - - -
298D MET* 4.7 0.9 - - + -
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA 2.9 19.2 + - - +
41D SER 3.1 6.5 + - - +
43D LEU* 1.3 73.4 - - - +
45D MET* 1.3 68.8 + - - +
47D GLN* 3.2 22.7 - - - +
62D MET* 3.7 12.3 - - + +
64D PHE* 4.2 4.7 - - + -
66D ILE* 3.6 32.6 - - + +
75D LEU* 4.2 14.8 - - + -
117D PHE* 3.9 4.4 - - + -
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Residues in contact with MET 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D SER* 3.1 12.4 + - - +
42D VAL* 3.0 16.9 + - - +
44D ALA* 1.3 75.8 - - - +
46D LEU* 1.3 52.4 + - - +
48D LEU* 2.8 36.6 + - - +
49D THR* 3.9 1.7 + - - +
95D ASP* 3.8 40.2 - - + +
96D ALA* 5.2 1.8 - - - -
97D ILE* 4.0 11.7 - - + -
113D PHE* 3.5 28.7 - - + -
117D PHE* 3.6 36.6 - - + +
119D SER* 3.9 21.8 - - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL 2.8 13.0 + - - +
43D LEU* 3.5 26.7 - - + +
45D MET* 1.3 76.8 - - - +
47D GLN* 1.3 57.9 + - - +
48D LEU 3.1 0.2 - - - -
49D THR* 3.0 26.8 + - + +
50D THR* 2.9 30.0 - - + +
58D ILE* 4.0 9.0 - - + -
97D ILE* 4.0 23.9 - - + +
163D LEU* 5.2 4.3 - - + -
165D LEU* 5.0 17.9 - - + -
298D MET* 3.6 31.9 - - + -
306D PHE* 4.1 11.9 - - + -
317D VAL* 4.5 10.8 - - + -
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU 3.1 12.9 + - - +
44D ALA* 3.2 17.0 - - - +
45D MET 2.8 0.8 + - - -
46D LEU* 1.3 76.2 - - - +
48D LEU* 1.3 61.0 + - - +
50D THR* 3.0 27.6 + - - +
55D GLN* 4.4 7.1 - - + +
58D ILE* 4.0 16.8 - - + -
59D GLN* 3.4 26.6 + - + +
62D MET* 3.4 25.3 - - - +
64D PHE* 3.3 21.8 + - - -
65D LYS* 3.3 9.4 - - - -
66D ILE* 2.9 35.9 + - + +
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D MET 2.8 10.8 + - - +
47D GLN* 1.3 80.9 - - - +
49D THR* 1.3 56.2 + - - +
50D THR 3.2 0.8 - - - +
66D ILE* 3.9 12.3 - - + -
67D ASP* 3.1 27.6 - - - +
109D PHE* 3.5 18.8 - - + -
112D HIS* 3.7 21.1 - - + +
113D PHE* 3.5 39.9 - - + +
116D LEU* 4.3 10.5 - - + -
117D PHE* 3.7 21.1 - - + -
308D SER* 3.1 22.9 + - - -
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Residues in contact with THR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D MET 4.4 4.3 - - - +
46D LEU* 3.0 24.5 + - + +
48D LEU* 1.3 76.1 - - - +
50D THR* 1.3 57.0 + - - +
97D ILE* 4.3 27.1 - - + -
109D PHE* 3.4 27.6 - - + -
113D PHE* 5.2 0.7 - - + -
121D VAL* 5.0 1.8 - - + -
163D LEU* 5.2 0.5 - - - +
306D PHE* 3.2 41.6 - - - +
308D SER* 3.7 1.8 - - - -
309D LEU* 3.3 30.7 + - + +
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Residues in contact with THR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 2.9 24.5 - - + +
47D GLN* 3.0 19.9 + - - +
48D LEU 3.2 1.0 - - - +
49D THR* 1.3 80.4 - - - +
51D GLY* 1.3 59.3 + - - +
54D THR* 4.3 3.8 - - + -
55D GLN* 2.8 38.7 + - - +
58D ILE* 4.4 11.4 - - + +
305D ASP 3.4 8.5 - - - -
306D PHE* 3.3 28.0 - - + -
308D SER* 2.9 18.8 + - - -
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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
------------------------------------------------------------
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