Contacts of the strand formed by residues 21 - 29 (chain B) in PDB entry 3M4D
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 LYS 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS 5.0 3.2 + - - -
47A ASN* 3.6 41.1 + - - +
48A HIS 5.7 1.0 - - - -
49A ASN* 6.3 0.2 - - - +
19B THR* 4.5 11.4 - - + +
20B VAL* 1.3 75.9 - - - +
22B THR* 1.3 64.6 + - - +
40B TYR* 4.2 1.1 - - - +
41B SER* 3.4 1.0 - - - -
42B PHE* 2.8 41.2 + - + +
288B LYS 5.2 4.3 + - - -
289B GLU* 3.4 48.2 + - + +
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Residues in contact with THR 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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12A THR 3.8 16.4 - - - +
13A ASP 5.2 2.5 - - - +
14A ILE* 3.8 7.6 - - + +
45A ASP* 5.1 1.4 + - - -
47A ASN 2.9 7.5 + - - +
48A HIS* 2.7 33.7 + - - +
49A ASN* 3.0 22.2 + - - +
20B VAL* 4.0 17.0 - - + +
21B LYS* 1.3 80.3 + - - +
23B GLY* 1.3 60.1 + - - +
39B PHE* 4.1 7.4 - - + -
40B TYR* 3.2 16.0 + - - -
41B SER* 3.5 19.7 - - - +
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Residues in contact with GLY 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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48A HIS* 3.4 7.8 + - - -
49A ASN* 3.1 17.3 - - - -
22B THR* 1.3 79.6 - - - +
24B ASP* 1.3 61.0 + - - -
39B PHE* 3.3 9.4 - - - -
40B TYR* 2.9 46.6 + - - -
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Residues in contact with ASP 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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48A HIS* 3.9 15.1 + - - +
49A ASN* 2.8 15.1 + - - +
50A LYS* 3.0 19.3 + - + -
52A LEU* 5.8 1.3 - - - +
99A SER* 2.5 24.9 + - - -
233A THR* 3.8 15.5 + - + +
23B GLY* 1.3 73.2 - - - -
25B LEU* 1.3 73.5 + - - +
26B VAL* 3.4 11.4 - - - +
37B LYS* 2.7 39.2 + - - +
38B VAL 3.4 2.0 - - - -
39B PHE* 3.8 12.5 - - - -
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Residues in contact with LEU 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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49A ASN* 3.6 15.3 - - - +
50A LYS* 4.2 8.3 - - - +
24B ASP* 1.3 92.6 + - - +
26B VAL* 1.3 62.3 + - - +
27B THR* 4.3 1.1 + - - -
36B LYS 3.8 0.9 - - - +
37B LYS* 3.3 2.8 - - - -
38B VAL* 2.9 39.7 + - + +
40B TYR* 4.0 17.3 - - + -
282B TYR* 3.9 35.2 + - + -
291B MET* 3.5 33.0 - - + +
292B THR* 4.3 3.6 - - + +
293B ASN* 3.6 21.1 - - - +
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Residues in contact with VAL 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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50A LYS* 4.4 6.2 - - - +
97A GLN* 3.2 28.0 + - - +
98A ILE 3.7 6.7 - - - +
99A SER* 3.8 17.5 - - - -
162A ASP* 3.8 18.2 - - + -
233A THR* 4.6 5.8 - - - +
24B ASP* 3.4 22.7 - - - +
25B LEU* 1.3 71.2 - - - +
27B THR* 1.3 70.2 + - - +
35B HIS* 3.6 25.6 - - + +
36B LYS 3.4 4.9 - - - +
37B LYS* 3.5 17.5 - - + -
293B ASN* 5.3 1.5 + - - +
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Residues in contact with THR 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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97A GLN* 4.9 1.6 - - - +
25B LEU 5.2 0.5 - - - -
26B VAL* 1.3 79.8 + - - +
28B TYR* 1.3 70.1 + - - +
29B ASP* 5.5 1.3 - - + -
34B MET 3.7 0.9 - - - +
35B HIS* 4.0 0.2 - - - -
36B LYS* 2.8 50.4 + - - +
280B GLU* 3.6 20.7 + - - +
282B TYR* 4.6 4.6 + - - -
293B ASN* 3.2 26.3 + - - -
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Residues in contact with TYR 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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160A PRO 3.7 8.5 + - - -
161A THR* 3.5 47.0 - - + +
162A ASP* 3.3 35.4 + - + +
27B THR* 1.3 81.0 - - - +
29B ASP* 1.3 62.6 + - - +
30B LYS* 3.6 45.2 + - + +
33B GLY* 3.8 15.2 - - - -
34B MET 3.3 29.8 - - - -
35B HIS* 3.7 4.5 - - + -
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Residues in contact with ASP 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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27B THR* 4.1 2.8 + - + +
28B TYR* 1.3 71.6 - - - +
30B LYS* 1.3 58.2 + - - +
31B GLU* 3.3 10.0 + - - +
32B ASN* 2.7 43.2 + - + -
33B GLY* 2.8 25.5 + - - -
34B MET* 2.9 23.0 + - + +
36B LYS* 4.8 4.3 - - - -
278B SER* 2.6 31.5 + - - +
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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