Contacts of the helix formed by residues 19 - 34 (chain B) in PDB entry 1VLM
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 HIS 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 2.8 61.3 + + + +
16B PHE 4.1 0.9 - - - -
18B VAL* 1.3 99.3 + - + +
20B ARG* 1.3 62.9 + - - +
21B PHE 3.4 2.5 - - - -
22B ALA* 3.2 8.5 + - + +
23B TYR* 3.0 21.0 + - - +
180B HIS* 6.0 1.1 - + - -
181B PRO* 3.8 25.1 + - + +
182B SER* 4.2 23.7 - - - -
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE 3.4 19.7 + - - +
17B LEU* 3.6 10.1 + - - +
18B VAL 3.5 2.8 + - - -
19B HIS* 1.3 76.4 - - - +
21B PHE* 1.3 67.2 + - + +
23B TYR* 3.2 17.8 + - + +
24B LEU* 2.9 62.1 + - + +
48B ARG* 6.1 0.6 - - - +
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B HIS 3.4 0.8 - - - -
20B ARG* 1.3 82.1 - - + +
22B ALA* 1.3 58.0 + - - +
24B LEU* 3.5 12.3 + - + +
25B SER* 2.7 34.3 + - - -
184B LEU* 3.4 38.1 - - + +
185B SER* 3.5 24.2 - - - -
186B GLU* 3.7 26.2 - - + +
187B ILE* 3.7 15.5 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 4.3 10.5 - - + -
19B HIS* 3.2 15.7 + - + +
21B PHE* 1.3 76.4 - - - +
23B TYR* 1.3 63.1 + - - +
25B SER* 3.2 5.3 + - - -
26B GLU* 3.0 29.6 + - - +
177B LEU* 4.1 17.3 - - + +
181B PRO* 4.1 20.1 + - + +
184B LEU* 3.5 19.2 - - + +
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.9 18.3 - - + -
16B PHE* 3.6 41.7 - + + +
19B HIS 3.0 12.8 + - - +
20B ARG* 3.3 28.5 - - - +
22B ALA* 1.3 76.5 - - - +
24B LEU* 1.3 67.1 + - + +
26B GLU* 3.3 6.1 + - - +
27B LEU* 3.0 40.2 + - + +
48B ARG* 2.5 53.1 + - + -
49B PHE* 4.3 11.0 - + - -
52B PRO* 3.8 10.9 - - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 2.9 64.5 + - + +
21B PHE* 4.0 9.0 - - + +
23B TYR* 1.3 84.2 - - + +
25B SER* 1.3 55.6 + - - +
27B LEU* 3.7 24.7 - - + +
28B GLN* 3.1 27.5 + - - +
187B ILE* 3.8 37.0 - - + +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE 2.7 22.9 + - - -
22B ALA* 3.3 9.9 - - - -
24B LEU* 1.3 75.8 - - - +
26B GLU* 1.3 64.6 + - - +
28B GLN* 3.4 3.4 + - - +
29B ALA* 3.0 17.8 + - - +
176B THR* 3.4 21.2 + - - +
177B LEU* 4.9 3.4 - - - -
187B ILE* 3.5 8.1 - - - +
188B GLU* 2.8 44.5 + - - +
190B VAL* 4.6 0.5 - - - +
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.8 27.4 - - - -
22B ALA 3.0 15.4 + - - +
23B TYR* 3.7 5.6 - - - +
25B SER* 1.3 76.4 - - - +
27B LEU* 1.3 60.9 + - - +
29B ALA* 3.3 2.6 + - - +
30B VAL* 3.0 26.9 + - - +
49B PHE* 3.8 22.4 - - + -
97B VAL* 5.1 0.7 - - - +
98B THR* 5.4 1.4 + - - -
128B VAL* 5.1 5.4 - - - +
176B THR* 4.9 0.4 - - + -
177B LEU* 3.8 20.4 - - + +
199B PHE* 3.6 52.8 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 3.0 28.1 + - + +
24B LEU* 3.7 32.1 - - + +
25B SER 3.3 0.2 - - - -
26B GLU* 1.3 77.5 - - - +
28B GLN* 1.3 52.4 + - - +
30B VAL* 3.3 4.1 + - - +
31B LYS* 2.7 37.0 + - + +
48B ARG 4.3 0.4 - - - +
49B PHE* 3.7 25.3 - - + -
52B PRO* 3.6 41.3 - - + -
53B LEU* 3.8 25.4 - - + +
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU 3.1 15.1 + - - +
25B SER* 3.6 8.3 - - - +
27B LEU* 1.3 79.3 - - - +
29B ALA* 1.3 62.7 + - - +
31B LYS* 3.3 17.3 + - - +
32B CYS* 3.1 33.1 + - - -
187B ILE* 4.5 20.6 - - + +
188B GLU 5.1 2.0 - - - +
190B VAL* 3.6 18.4 - - + -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 3.0 16.6 + - - +
26B GLU 3.7 4.9 - - - +
27B LEU 3.3 0.2 - - - -
28B GLN* 1.3 73.7 - - - +
30B VAL* 1.3 65.6 + - - +
32B CYS* 3.3 14.9 + - - +
33B LEU 3.7 2.3 + - - -
174B VAL* 3.7 13.2 - - + +
175B GLN 5.0 0.4 - - - -
176B THR* 3.8 21.3 - - + +
190B VAL* 3.8 22.8 - - + +
199B PHE* 4.4 2.2 - - + +
201B VAL* 3.7 20.2 - - + +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU 3.0 17.2 + - - +
27B LEU* 3.7 7.9 - - - +
29B ALA* 1.3 73.9 - - - +
31B LYS* 1.3 63.6 + - - +
33B LEU* 2.9 14.9 + - - +
34B LEU* 3.1 18.2 + - + +
49B PHE* 4.8 4.0 - - + -
53B LEU* 3.4 30.3 - - + -
95B LEU* 3.8 19.5 - - + -
97B VAL* 4.0 22.2 - - + -
124B ILE* 4.7 3.2 - - + +
126B GLY* 5.3 1.1 - - - -
199B PHE* 4.3 6.1 - - + -
201B VAL* 4.0 25.6 - - + -
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 2.7 21.8 + - + +
28B GLN* 3.7 20.2 - - - +
29B ALA 3.3 0.2 - - - -
30B VAL* 1.3 72.6 - - - +
32B CYS* 1.3 62.8 + - - +
33B LEU 3.3 0.9 + - - -
34B LEU* 3.3 23.4 + - + +
52B PRO 5.5 4.0 - - - +
53B LEU* 4.0 20.4 - - + -
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Residues in contact with CYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLN* 3.1 28.4 + - - -
29B ALA* 3.4 10.8 - - - +
30B VAL 3.1 0.2 - - - -
31B LYS* 1.3 78.0 - - - +
33B LEU* 1.3 65.6 + - + +
34B LEU 5.0 1.0 - - - +
174B VAL* 4.8 6.5 - - + -
190B VAL* 4.0 28.3 - - + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA 3.7 0.6 + - - +
30B VAL 2.9 8.2 + - - +
32B CYS* 1.3 82.2 - - + +
34B LEU* 1.3 65.2 + - - +
35B PRO* 3.3 2.9 - - - +
124B ILE* 3.9 9.1 - - + +
172B LYS* 3.7 48.9 - - + +
174B VAL* 3.8 29.4 - - + +
201B VAL* 3.6 41.3 - - + +
203B ARG* 3.3 40.7 + - + +
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.1 28.5 + - + +
31B LYS* 3.3 17.4 + - + +
32B CYS 5.0 1.0 - - - +
33B LEU* 1.3 77.6 - - - +
35B PRO* 1.3 67.6 - - - +
53B LEU* 3.9 44.6 - - + +
55B ILE* 4.6 4.5 - - + -
93B PHE* 3.6 37.9 - - + -
95B LEU* 4.7 7.2 - - + -
124B ILE* 4.2 11.7 - - + -
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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