Contacts of the strand formed by residues 31 - 37 (chain M) in PDB entry 1ZGL
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 SER 31 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 5.0 3.3 - - - +
29M TYR 4.4 0.7 + - - -
30M PRO* 1.3 76.5 + - - +
32M LEU* 1.3 64.5 + - - +
33M PHE* 3.5 11.6 - - - -
49M ALA 3.5 12.8 - - - -
50M THR* 3.3 28.3 + - - +
92M LEU* 2.9 4.7 - - - +
93M SER* 2.6 43.9 + - - -
100P VAL 5.3 0.2 + - - -
101P ASN* 4.1 14.0 + - - +
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Residues in contact with LEU 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M CYS* 5.9 0.4 - - - -
24M TYR* 3.9 31.4 - - + +
30M PRO* 4.5 3.1 - - + -
31M SER* 1.3 83.1 - - - +
33M PHE* 1.3 71.7 + - - +
48M LYS 3.4 14.7 - - - -
49M ALA* 3.0 15.7 + - - +
66M TYR* 3.5 44.6 - - + +
72M SER 5.1 0.9 - - - +
73M PHE* 3.7 40.2 - - + -
90M CYS* 5.5 3.1 - - - -
91M ALA 3.1 9.9 - - - +
92M LEU* 3.8 16.4 - - + -
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Residues in contact with PHE 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M SER* 3.5 26.0 - - - -
32M LEU* 1.3 80.9 - - - +
34M TRP* 1.3 66.4 + - - +
35M TYR* 4.2 24.2 - + + -
45M LEU* 4.4 13.5 - - + -
47M LEU 2.9 11.2 - - - +
48M LYS* 4.3 17.0 - - + -
49M ALA 5.6 0.2 - - - -
50M THR* 5.8 3.1 - - + -
73M PHE* 3.8 8.0 - - - -
90M CYS* 3.6 3.5 - - - -
91M ALA* 2.7 48.1 + - + +
92M LEU 4.1 2.2 - - - -
93M SER* 3.5 32.8 - - - -
104M LEU* 4.1 8.5 - - + -
102P THR 3.7 11.9 - - - -
103P GLU* 3.7 23.8 - - - -
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Residues in contact with TRP 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M GLN* 3.4 25.6 - - - -
20M ILE* 3.4 29.2 - - + -
21M ASN 4.6 1.6 - - - -
22M CYS* 3.9 4.7 - - + -
33M PHE* 1.3 73.0 - - - +
35M TYR* 1.3 64.2 + - - +
46M LEU* 2.8 35.7 + - + +
47M LEU* 2.9 31.5 + - + +
64M ALA* 4.1 11.9 - - + +
73M PHE* 2.7 58.6 + + - -
75M LEU* 3.6 25.9 - - + +
88M TYR* 3.5 31.9 - + + -
89M PHE 3.2 21.5 - - - -
90M CYS* 3.5 15.7 - - + -
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Residues in contact with TYR 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M PHE* 4.5 16.2 - - + -
34M TRP* 1.3 77.5 - - - +
36M VAL* 1.3 58.9 + - - +
43M LEU* 4.3 20.6 - - + -
44M GLN 3.0 9.9 - - - +
45M LEU* 3.1 50.0 - - + +
46M LEU* 4.7 0.7 - - - -
87M VAL 4.1 0.2 - - - +
88M TYR* 3.5 3.9 - - - +
89M PHE* 2.6 53.1 + - + +
91M ALA* 4.8 4.7 - - + -
104M LEU* 3.5 32.1 - - + +
106M PHE* 3.5 25.6 - + - -
103P GLU 3.9 4.2 + - - -
106P ALA 2.6 28.5 + - - -
107P PHE* 6.1 0.2 - - - -
108P PHE* 4.3 8.7 - + - -
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Residues in contact with VAL 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M TRP 4.2 0.6 + - - -
35M TYR* 1.3 73.9 - - - +
37M GLN* 1.3 62.0 + - - +
38M TYR* 3.7 31.2 - - + +
42M GLY 3.7 0.9 - - - +
43M LEU* 4.5 1.1 - - - -
44M GLN* 2.7 61.7 + - + +
45M LEU 4.9 3.8 - - - +
46M LEU* 4.5 11.5 - - + +
86M ALA* 3.6 22.2 - - + -
87M VAL 3.4 12.3 - - - +
88M TYR* 3.7 25.6 - - + -
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Residues in contact with GLN 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M TYR 4.2 0.4 + - - -
36M VAL* 1.3 74.2 - - - +
38M TYR* 1.3 70.5 + - - +
41M GLU 3.4 21.6 - - - +
42M GLY* 3.4 6.1 - - - +
43M LEU* 2.9 31.1 - - + +
86M ALA* 3.9 2.2 - - - -
87M VAL* 2.9 44.5 + - + +
89M PHE* 3.8 17.1 - - + -
111M ARG* 5.2 0.2 + - - -
37P GLN* 2.5 40.8 + - - +
89P LEU* 5.1 0.6 - - - +
91P LEU* 5.2 0.3 - - - +
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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