Contacts of the helix formed by residues 19 - 31 (chain B) in PDB entry 5LN3
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 LEU 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 3.7 13.0 - - + -
12B THR 4.0 20.2 - - - +
13B PHE* 4.4 22.4 - - + +
17B GLY 5.2 3.6 - - - +
18B LYS* 1.3 84.5 - - - +
20B VAL* 1.3 62.8 + - - +
21B GLN 3.4 1.1 - - - -
22B ILE* 3.3 32.5 + - + +
23B GLU* 3.1 25.5 + - - +
122B THR* 5.6 4.5 - - + -
79C ILE* 6.2 4.7 - - + -
128C ARG* 5.0 14.4 - - - +
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Residues in contact with VAL 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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10B LEU 4.8 4.0 - - - +
11B THR* 4.3 1.9 - - - +
12B THR* 4.5 22.9 + - - +
14B SER* 4.9 8.0 + - - +
18B LYS* 3.9 3.0 + - - -
19B LEU* 1.3 71.7 - - - +
21B GLN* 1.4 81.7 + - + +
23B GLU* 3.2 19.8 + - + +
24B TYR* 3.2 37.6 + - + +
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Residues in contact with GLN 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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15A ILE* 3.4 28.6 - - - +
16A PHE* 3.2 49.5 + - + +
10B LEU* 3.7 9.0 - - - +
11B THR* 3.6 38.3 + - + +
19B LEU 3.4 0.6 - - - -
20B VAL* 1.4 82.7 - - + +
22B ILE* 1.4 60.2 - - + +
24B TYR* 3.1 24.8 + - - +
25B ALA* 3.2 10.1 + - - +
128B ARG* 3.6 23.9 - - - +
129B PRO* 5.2 7.0 - - + +
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Residues in contact with ILE 22 (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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11B THR* 4.2 8.1 - - + +
19B LEU* 3.3 40.8 - - + +
21B GLN* 1.4 72.6 - - + +
23B GLU* 1.3 70.0 + - - +
25B ALA* 3.2 20.9 + - + +
26B LEU* 3.6 14.2 + - + +
122B THR* 4.6 20.2 - - + +
129B PRO* 5.2 12.8 - - + -
151B PRO 4.9 5.6 - - - +
152B SER* 4.2 38.4 - - - +
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Residues in contact with GLU 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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18B LYS* 4.2 28.4 - - + +
19B LEU* 3.1 20.2 + - - +
20B VAL* 3.3 13.5 - - + +
22B ILE* 1.3 82.7 - - - +
24B TYR* 1.3 68.3 + - + +
26B LEU* 3.3 34.8 + - - +
27B ALA* 3.7 3.3 + - - +
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Residues in contact with TYR 24 (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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15A ILE* 5.4 5.4 - - + -
16A PHE* 3.5 35.9 - - + -
17A SER* 3.8 8.7 - - - +
18A PRO* 3.3 46.6 - - + +
20B VAL* 3.2 38.4 + - + +
21B GLN* 3.1 18.6 + - - +
23B GLU* 1.3 83.8 - - + +
25B ALA* 1.4 51.4 + - - +
27B ALA* 2.8 31.3 + - + +
28B ALA* 3.0 10.0 + - - +
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Residues in contact with ALA 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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16A PHE* 4.9 11.4 - - + -
21B GLN 3.2 9.7 + - - +
22B ILE* 3.2 14.8 + - + +
24B TYR* 1.4 72.6 - - - +
26B LEU* 1.4 58.6 + - + +
28B ALA* 2.8 24.7 + - - +
29B VAL* 2.8 21.8 + - - +
130B PHE 5.3 0.9 - - - +
131B GLY* 4.6 10.3 - - - -
151B PRO* 4.2 25.4 - - + -
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Residues in contact with LEU 26 (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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22B ILE* 3.6 20.0 - - + +
23B GLU* 3.3 25.5 + - - +
25B ALA* 1.4 77.2 - - + +
27B ALA* 1.4 56.2 + - - +
29B VAL* 3.4 12.2 - - + +
30B ALA* 3.2 24.2 + - - +
150B ASP* 5.7 2.7 - - - +
151B PRO* 5.1 7.6 - - + -
152B SER* 4.4 17.0 - - - +
167B TYR* 5.1 15.3 + - - +
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Residues in contact with ALA 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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17A SER 5.6 1.1 - - - +
18A PRO* 5.5 12.6 - - + -
23B GLU 3.7 1.7 + - - +
24B TYR* 2.8 19.8 + - + +
26B LEU* 1.4 61.0 - - - +
28B ALA* 1.3 58.2 + - - +
29B VAL 3.2 0.4 - - - -
30B ALA* 3.0 27.2 + - + +
31B GLY* 3.5 4.7 + - - -
416K PHE* 4.8 2.8 - - - -
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Residues in contact with ALA 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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16A PHE* 5.1 9.2 - - + -
24B TYR 3.0 6.1 + - - +
25B ALA* 2.8 20.6 + - + +
27B ALA* 1.3 76.3 - - - +
29B VAL* 1.4 59.2 + - - +
31B GLY* 3.7 1.7 + - - -
32B GLY 4.4 0.3 + - - -
78B GLY* 4.2 11.2 - - - -
79B MET* 4.4 19.0 - - + +
131B GLY* 4.1 18.2 - - - +
416K PHE* 3.6 27.0 - - - -
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Residues in contact with VAL 29 (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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25B ALA 2.8 17.2 + - - +
26B LEU* 3.4 11.2 - - - +
28B ALA* 1.4 71.8 - - - +
30B ALA* 1.4 65.1 - - - +
31B GLY 3.2 0.4 - - - -
32B GLY* 3.2 15.0 + - - -
77B SER* 3.9 18.1 - - - +
78B GLY* 4.4 6.1 - - - -
131B GLY 4.4 6.3 - - - +
132B VAL 4.1 5.4 - - - -
133B SER* 3.5 30.7 - - - +
151B PRO* 4.0 22.9 - - + -
163B MET* 5.6 2.5 - - + -
164B GLY* 4.2 7.5 + - - +
167B TYR* 5.9 6.5 - - + -
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Residues in contact with ALA 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 LEU 3.2 13.5 + - - +
27B ALA* 3.0 19.1 + - + +
29B VAL* 1.4 80.0 - - - +
31B GLY* 1.4 53.6 - - - +
164B GLY 3.7 4.7 - - - +
165B LYS* 3.2 34.3 + - - +
166B ASN 4.8 0.4 + - - +
167B TYR* 4.5 18.8 - - + -
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Residues in contact with GLY 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 ALA 3.5 5.2 + - - -
28B ALA 3.7 0.4 + - - -
29B VAL 3.2 1.0 - - - -
30B ALA* 1.4 76.9 - - - +
32B GLY* 1.4 63.5 + - - +
165B LYS* 3.3 21.9 + - - -
416K PHE* 3.8 35.1 - - - +
417K TYR* 3.7 4.7 + - - -
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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