Contacts of the helix formed by residues 32 - 46 (chain A) in PDB entry 3VLN
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A MET* 3.1 21.9 + - - +
31A PHE* 1.3 76.7 - - - +
33A PRO* 1.3 62.2 - - - +
34A PHE* 3.3 4.5 + - - +
35A ALA* 3.1 25.5 + - - +
36A GLU* 2.9 27.4 + - - +
39A ARG* 5.1 1.7 + - - -
72A VAL* 3.9 10.3 - - - +
183A ARG* 3.7 1.5 + - - -
908A ACT 2.7 34.1 + - - -
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Residues in contact with PRO 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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31A PHE 3.4 9.6 - - - +
32A SER* 1.3 80.9 - - - +
34A PHE* 1.3 71.5 - - + +
36A GLU* 3.3 3.7 + - + +
37A ARG* 3.3 19.6 + - - +
179A PRO* 3.5 29.5 - - + +
180A TRP* 3.7 31.3 - - + +
183A ARG* 3.7 28.0 - - - +
908A ACT 4.1 13.7 - - + +
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Residues in contact with PHE 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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32A SER* 3.3 5.0 + - - +
33A PRO* 1.3 81.4 - - + +
35A ALA* 1.3 61.7 + - - +
37A ARG* 3.3 25.1 + - - +
38A THR 3.9 0.3 + - - -
72A VAL 4.0 0.2 - - - +
73A PRO* 3.8 5.0 - - + +
86A SER* 3.4 15.6 - - - -
124A PRO* 4.1 19.3 - - + -
180A TRP* 3.6 32.3 - + - -
904A ASC 3.1 82.8 - - - +
908A ACT 3.5 22.4 - - + -
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Residues in contact with ALA 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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26A ILE* 4.1 0.6 - - + +
28A SER* 3.3 30.5 - - - +
29A MET 4.1 6.1 - - - +
32A SER* 3.1 25.0 + - - +
34A PHE* 1.3 73.6 - - - +
36A GLU* 1.3 65.0 + - - +
38A THR* 3.2 5.5 + - - -
39A ARG* 3.1 25.5 + - - +
72A VAL* 4.3 4.5 - - + -
73A PRO* 3.8 21.4 - - + +
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Residues in contact with GLU 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 SER 2.9 15.5 + - - +
33A PRO 3.5 9.2 - - - +
34A PHE 3.2 0.4 - - - -
35A ALA* 1.3 76.8 - - - +
37A ARG* 1.3 62.1 + - - +
39A ARG* 3.7 25.2 - - - +
40A LEU* 2.8 37.1 + - + +
178A TRP* 4.2 6.6 + - - -
179A PRO* 3.4 12.2 - - + +
182A GLU* 2.5 25.9 - - - +
183A ARG* 2.8 35.1 + - - +
212A VAL 5.6 0.3 - - - +
215A LEU* 4.0 20.6 - - + +
216A LEU* 5.4 0.2 - - - +
217A THR* 6.1 0.2 - - - -
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Residues in contact with ARG 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 PRO 3.3 10.7 + - - +
34A PHE* 3.3 14.4 + - - +
35A ALA 3.2 0.4 - - - -
36A GLU* 1.3 79.2 - - - +
38A THR* 1.3 62.5 + - - +
40A LEU* 3.3 11.0 + - - +
41A VAL* 3.1 25.3 + - - +
86A SER* 2.8 40.6 + - - -
87A ALA* 4.4 9.5 - - - +
90A CYS* 3.6 13.4 - - - -
117A LEU* 3.7 24.3 - - - +
120A PHE* 3.7 17.4 - - - -
124A PRO* 5.1 2.8 - - - +
175A TYR* 4.2 5.9 - - - +
176A LEU* 2.8 50.1 + - + +
179A PRO* 4.2 4.0 - - + +
180A TRP* 3.5 14.5 - - - -
904A ASC 3.9 7.9 + - - -
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Residues in contact with THR 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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26A ILE* 3.7 21.5 - - + -
34A PHE 4.0 1.0 + - - -
35A ALA 3.2 7.7 + - - -
37A ARG* 1.3 77.2 - - - +
39A ARG* 1.3 57.9 + - - +
41A VAL* 3.2 3.9 + - - +
42A LEU* 2.9 28.8 + - + +
73A PRO* 3.2 18.5 - - + +
75A LEU* 3.9 14.6 - - + -
86A SER 4.0 2.6 + - - -
89A THR* 2.7 29.3 + - - +
90A CYS* 3.8 7.4 - - - -
93A LEU* 3.7 21.5 - - + +
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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
----------------------------------------------------------
26A ILE* 3.7 21.1 - - + -
28A SER* 3.5 25.1 + - - -
29A MET 4.9 2.2 + - - -
30A ARG* 3.6 24.6 + - - +
32A SER 5.1 0.6 + - - -
35A ALA 3.1 14.8 + - - +
36A GLU* 3.2 30.1 + - - +
38A THR* 1.3 73.1 - - - +
40A LEU* 1.3 65.3 + - - +
42A LEU* 3.4 9.6 + - + +
43A LYS* 3.0 24.9 + - - +
49A HIS* 5.8 0.5 + - - -
51A VAL* 5.1 3.1 - - - -
183A ARG* 6.0 0.2 - - - +
215A LEU* 3.6 27.5 + - + +
217A THR* 5.7 1.4 + - - -
901A SO4 3.0 43.1 + - - +
905A GOL 3.7 20.4 + - - -
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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 GLU* 2.8 38.0 + - + +
37A ARG* 3.5 4.5 - - - +
39A ARG* 1.3 76.1 - - - +
41A VAL* 1.3 57.6 + - - +
43A LYS 3.4 0.3 + - - -
44A ALA* 2.8 31.6 + - - +
175A TYR* 3.7 46.0 - - + +
178A TRP* 4.3 11.4 - - + -
179A PRO* 4.1 7.9 - - + -
211A THR* 3.4 22.4 - - + +
212A VAL* 3.9 22.9 - - + -
215A LEU* 3.6 20.4 - - + +
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Residues in contact with VAL 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 ARG 3.1 14.4 + - - +
38A THR 3.6 7.0 - - - +
40A LEU* 1.3 73.7 - - - +
42A LEU* 1.3 64.9 + - - +
44A ALA* 3.3 4.8 + - - -
45A LYS* 3.0 33.1 + - + +
90A CYS* 3.7 28.3 - - - +
93A LEU* 3.9 28.5 - - + -
102A LEU* 3.9 18.6 - - + -
172A MET* 3.7 21.5 - - + -
175A TYR* 4.8 8.5 - - + -
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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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24A ILE* 4.0 10.5 - - + -
26A ILE* 4.1 23.8 - - + -
38A THR* 2.9 28.5 + - + +
39A ARG* 3.4 12.1 + - + +
41A VAL* 1.3 71.3 - - - +
43A LYS* 1.3 61.8 + - - +
45A LYS 3.8 0.2 - - - -
46A GLY* 3.1 3.3 + - - -
47A ILE* 3.0 59.0 + - + +
49A HIS* 3.8 38.5 - - + +
75A LEU* 4.8 2.5 - - + -
93A LEU* 3.6 26.0 - - + -
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Residues in contact with LYS 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 3.0 17.6 + - - +
40A LEU 3.8 2.7 - - - +
42A LEU* 1.3 75.6 - - - +
44A ALA* 1.3 65.8 + - - +
46A GLY* 3.0 13.1 + - - -
49A HIS* 5.2 7.6 - - + -
210A PRO 5.1 0.4 - - - +
211A THR* 3.8 21.5 + - + +
214A ALA* 3.6 27.5 - - + +
215A LEU* 3.3 25.0 - - + +
901A SO4 4.7 11.2 + - - -
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Residues in contact with ALA 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 2.8 22.3 + - - +
41A VAL 3.8 3.1 - - - +
43A LYS* 1.3 73.3 - - - +
45A LYS* 1.3 59.9 + - - +
46A GLY 3.7 0.2 + - - -
100A LYS* 4.5 17.8 + - + +
102A LEU* 4.3 16.4 - - + -
175A TYR* 4.0 24.5 - - + +
211A THR* 3.6 17.4 + - - +
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Residues in contact with LYS 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 VAL* 3.0 29.5 + - + +
44A ALA* 1.3 77.9 - - - +
46A GLY* 1.3 63.5 + - - +
47A ILE* 3.3 17.3 + - + +
93A LEU 3.6 24.7 - - - +
94A ASP* 2.8 34.1 + - - +
97A TYR* 3.7 11.5 + - - -
98A PRO 3.5 27.6 + - - +
99A GLY* 4.3 6.1 + - - -
100A LYS 2.8 39.3 + - - +
101A LYS* 3.9 4.9 - - - +
102A LEU* 4.1 9.4 - - + -
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Residues in contact with GLY 46 (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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42A LEU 3.1 3.0 + - - -
43A LYS* 3.0 14.8 + - - -
44A ALA 3.4 0.8 + - - -
45A LYS* 1.3 79.0 - - - +
47A ILE* 1.3 62.1 + - - +
48A ARG 3.7 2.3 + - - -
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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