Contacts of the strand formed by residues 29 - 40 (chain A) in PDB entry 4NEH
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 TRP 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLN* 3.6 0.3 - - - -
25A TYR* 2.9 60.6 + + + +
26A ALA* 4.9 2.7 - - + +
28A SER* 1.3 106.8 - - - +
30A VAL* 1.3 61.5 + - - +
31A VAL* 3.9 1.6 - - + +
49A GLN* 4.0 51.8 + - + -
50A CYS 3.4 7.0 - - - +
51A GLY* 4.0 24.2 - - - -
54A THR* 6.0 2.2 - - - -
575A LEU* 3.3 13.4 - - - +
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Residues in contact with VAL 30 (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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11A PHE* 4.6 9.4 - - + -
22A VAL* 4.3 5.6 - - + -
23A VAL 3.7 8.1 - - - +
24A GLN* 4.8 2.0 - - + -
29A TRP* 1.3 71.5 - - - +
31A VAL* 1.3 65.2 + - - +
32A VAL* 3.8 18.6 - - + -
49A GLN* 3.5 1.2 - - - -
50A CYS* 2.8 48.9 + - + +
575A LEU* 3.5 21.8 - - + -
584A ALA* 4.0 26.5 - - + -
591A VAL* 4.0 16.4 - - + -
593A LEU* 4.0 11.7 - - + -
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Residues in contact with VAL 31 (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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22A VAL* 3.4 2.3 - - - +
23A VAL* 2.8 41.7 + - + +
25A TYR* 3.7 31.0 - - + -
29A TRP* 4.7 1.1 - - + -
30A VAL* 1.3 72.2 - - - +
32A VAL* 1.3 61.5 + - - +
47A LEU* 4.5 13.2 - - + -
48A TYR 3.2 11.4 - - - +
49A GLN* 4.6 5.6 - - + -
60A ILE* 4.4 13.7 - - + -
77A LEU* 3.4 20.2 - - + +
86A LEU* 3.8 32.3 - - + -
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Residues in contact with VAL 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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18A PHE* 3.6 22.9 - - + -
19A GLY* 3.4 29.6 - - - +
21A SER 3.5 5.4 - - - +
22A VAL* 4.1 2.2 - - + -
30A VAL* 3.8 22.9 - - + +
31A VAL* 1.3 79.9 - - - +
33A GLY* 1.3 63.3 + - - +
46A GLY 4.0 0.2 - - - +
47A LEU* 3.6 3.5 - - - +
48A TYR* 2.8 39.2 + - + +
50A CYS* 3.9 13.5 - - - -
77A LEU* 4.3 2.2 - - - -
591A VAL* 3.6 25.8 - - + -
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Residues in contact with GLY 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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17A GLY 3.1 13.0 - - - +
18A PHE* 3.6 1.1 - - - -
19A GLY 3.3 14.6 + - - -
20A ASP 3.9 3.1 + - - -
21A SER* 2.9 25.3 + - - +
32A VAL* 1.3 75.4 - - - +
34A ALA* 1.3 60.2 + - - -
35A PRO* 3.6 6.5 - - - +
46A GLY 3.6 5.2 - - - -
47A LEU* 4.3 3.1 - - - -
74A GLY* 3.7 14.1 - - - -
77A LEU* 3.9 2.0 - - - +
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Residues in contact with ALA 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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15A SER* 4.0 20.0 - - - -
16A ALA 3.4 13.5 - - - +
17A GLY 3.4 3.6 - - - -
18A PHE* 3.7 14.1 - - + +
33A GLY* 1.3 73.7 - - - +
35A PRO* 1.3 67.6 - - - +
36A GLN 3.1 4.2 + - - -
37A LYS* 3.1 10.3 + - + +
46A GLY 2.8 31.7 + - - +
48A TYR* 4.1 9.4 - - + -
73A LEU 4.0 1.2 + - - -
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Residues in contact with PRO 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLY* 3.2 18.4 - - - +
20A ASP* 4.1 13.5 - - + +
33A GLY 3.6 2.9 - - - +
34A ALA* 1.3 86.7 - - - +
36A GLN* 1.3 64.2 + - + +
37A LYS 3.4 0.2 - - - -
44A THR* 3.8 4.0 - - - -
45A GLY* 3.2 16.3 + - - -
72A SER* 3.3 32.8 + - - +
73A LEU 3.5 12.3 - - - +
74A GLY 3.8 2.5 - - - +
75A LEU* 3.7 43.1 - - + +
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Residues in contact with GLN 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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16A ALA* 3.3 20.1 + - + +
17A GLY* 3.9 19.0 + - - -
20A ASP* 4.8 7.2 + - - +
34A ALA 3.2 0.8 - - - -
35A PRO* 1.3 85.0 - - + +
37A LYS* 1.3 65.0 + - - +
38A ILE* 3.4 17.2 + - - +
44A THR* 4.7 6.4 - - - +
45A GLY 4.5 0.2 - - - -
72A SER* 6.2 0.2 - - - +
588A ARG* 5.5 4.9 + - - -
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Residues in contact with LYS 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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15A SER* 3.2 23.7 + - - +
16A ALA* 3.1 22.6 + - - +
34A ALA 3.1 14.0 + - - +
36A GLN* 1.3 75.3 - - - +
38A ILE* 1.3 65.5 + - - +
39A THR* 3.3 30.7 + - + +
44A THR* 3.2 2.3 - - - -
45A GLY 2.6 29.5 + - - -
46A GLY* 4.3 10.8 - - - +
48A TYR* 3.2 23.8 + - + +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 5.8 2.7 - - + -
36A GLN 3.6 13.9 - - - +
37A LYS* 1.3 77.8 + - - +
39A THR* 1.3 61.7 + - - +
40A ALA* 3.3 24.2 - - - +
42A ASP 5.6 0.4 - - - +
43A GLN 3.6 7.2 - - - +
44A THR* 4.3 13.5 - - + +
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Residues in contact with THR 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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37A LYS* 3.3 31.6 + - + +
38A ILE* 1.3 72.4 - - - +
40A ALA* 1.3 63.9 + - - +
43A GLN* 3.3 25.8 + - - +
44A THR 4.6 0.2 - - - -
45A GLY 3.2 28.9 + - - +
46A GLY* 4.1 4.3 - - - -
64A VAL* 6.0 1.2 - - - +
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Residues in contact with ALA 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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38A ILE* 3.3 20.6 - - - +
39A THR* 1.3 82.1 + - - +
41A ALA* 1.3 65.6 + - - +
42A ASP 3.2 3.1 + - - -
43A GLN* 3.3 35.2 + - + +
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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