Contacts of the strand formed by residues 45 - 54 (chain B) in PDB entry 6MZL
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 VAL 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ILE* 3.7 32.5 - - + -
36B ASN 4.2 3.4 - - - -
37B ASN 4.4 0.9 - - - -
38B ILE* 3.7 26.9 - - + -
44B SER* 1.3 86.5 + - - +
46B VAL* 1.3 71.0 - - - +
151B SER* 3.3 2.6 - - - -
152B LEU* 2.8 54.5 + - + +
153B ASP 4.3 0.4 + - - -
159B LEU* 5.3 5.8 - - + -
161B PHE* 4.3 14.1 - - + -
189B TRP* 5.9 1.6 - - - +
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Residues in contact with VAL 46 (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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35B ILE* 3.7 4.5 - - - -
36B ASN* 2.8 47.8 + - + +
37B ASN* 3.6 31.2 + - + +
44B SER* 5.0 4.0 - - - +
45B VAL* 1.3 84.5 - - - +
47B GLY* 1.3 59.8 + - - +
73B TYR* 4.7 11.2 - - + +
149B ASN* 5.3 2.9 - - - +
150B PHE* 3.7 8.1 - - - +
151B SER* 3.9 14.8 - - - -
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Residues in contact with GLY 47 (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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33B VAL* 6.3 0.9 - - - -
34B CYS 3.2 15.3 - - - -
35B ILE* 4.7 0.4 - - - -
36B ASN* 4.6 1.8 - - - -
45B VAL* 5.7 0.2 - - - -
46B VAL* 1.3 78.5 - - - +
48B PHE* 1.3 63.0 + - - -
149B ASN* 3.4 5.3 + - - +
150B PHE* 2.8 51.3 + - - +
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Residues in contact with PHE 48 (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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32B VAL* 3.9 10.0 - - + +
33B VAL* 4.0 0.9 - - - +
34B CYS* 3.4 55.7 + - + -
36B ASN* 3.8 11.9 - - - -
47B GLY* 1.3 75.2 - - - +
49B VAL* 1.3 59.8 + - - +
50B GLU* 4.5 13.0 - - + -
147B HIS* 3.4 34.3 - + + +
148B ILE 2.9 12.8 - - - +
149B ASN* 4.3 6.7 - - + +
150B PHE* 3.9 2.7 - - - -
205B GLU* 4.5 6.3 - - - -
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Residues in contact with VAL 49 (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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31B GLN* 3.3 32.3 - - + +
32B VAL 3.3 15.3 - - - +
33B VAL* 5.0 3.4 - - + -
48B PHE* 1.3 74.9 - - - +
50B GLU* 1.3 65.9 + - - +
51B LEU* 3.7 17.3 - - + -
146B ILE 3.2 0.3 - - - +
147B HIS* 3.2 4.9 + - - -
148B ILE* 2.8 51.8 + - + -
150B PHE* 3.5 24.0 - - + -
190B PHE* 4.6 8.5 - - + -
191B PRO* 5.1 8.5 - - + +
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Residues in contact with GLU 50 (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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31B GLN* 3.3 9.5 - - - +
32B VAL* 3.1 43.3 + - + +
48B PHE* 4.5 11.8 - - + -
49B VAL* 1.3 79.7 - - - +
51B LEU* 1.3 62.3 + - - +
52B THR* 5.2 1.1 + - - -
76B ARG* 4.6 3.8 + - - -
145B LYS* 5.9 5.8 - - + +
146B ILE 2.6 13.0 - - - +
147B HIS* 2.9 35.9 + - + +
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Residues in contact with LEU 51 (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 LEU* 5.5 15.5 - - + -
30B HIS 3.7 4.3 - - - +
31B GLN* 4.2 15.0 - - + +
49B VAL* 3.7 33.0 - - + -
50B GLU* 1.3 80.3 - - - +
52B THR* 1.3 64.8 + - - +
53B ILE* 4.0 1.3 - - + -
65B LEU* 3.7 37.9 - - + -
144B LEU 3.6 0.7 - - - +
145B LYS* 3.1 10.6 - - - +
146B ILE* 2.8 59.4 + - + +
148B ILE* 4.9 0.9 - - + -
192B CYS* 6.0 0.2 - - - -
193B VAL* 6.3 1.1 - - + -
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Residues in contact with THR 52 (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 LEU* 3.6 5.9 - - - +
29B THR* 3.0 49.3 + - + +
30B HIS* 3.0 33.0 + - + +
50B GLU 5.2 0.9 + - - -
51B LEU* 1.3 74.3 + - - +
53B ILE* 1.3 60.7 + - - +
54B PHE* 5.4 9.2 - - + -
143B VAL* 5.9 3.1 - - + -
144B LEU 3.6 6.5 - - - +
145B LYS* 4.9 10.8 - - + +
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Residues in contact with ILE 53 (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 TYR* 3.6 28.7 - - + -
27B LYS 3.7 4.7 - - - +
28B LEU* 3.6 21.1 - - + -
51B LEU* 4.7 1.3 - - + +
52B THR* 1.3 74.9 - - - +
54B PHE* 1.3 71.4 + - - +
55B PRO* 3.4 22.0 - - + +
63B ILE* 4.9 17.3 - - + -
65B LEU* 6.6 0.2 - - + -
144B LEU* 2.9 58.0 + - + +
146B ILE* 4.1 28.0 - - + -
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Residues in contact with PHE 54 (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 LYS* 2.8 48.0 + - + +
28B LEU* 4.8 0.2 - - - +
29B THR* 4.3 25.5 - - + +
52B THR* 4.3 8.5 + - + -
53B ILE* 1.3 80.4 - - - +
55B PRO* 1.3 68.1 - - - +
142B LYS 3.3 5.2 - - - +
143B VAL* 3.5 39.7 - - + -
488B PHE* 4.8 12.6 - + - -
490B SER* 4.7 15.0 - - - -
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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