Contacts of the strand formed by residues 38 - 47 (chain A) in PDB entry 1PQA
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 GLY 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A SER* 3.1 7.1 - - - -
35A ARG 2.8 31.9 + - - +
36A ASN 3.2 2.2 + - - -
37A GLY* 1.3 82.7 - - - +
39A PRO* 1.3 75.7 - - - +
75A ARG* 5.3 0.2 - - - -
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Residues in contact with PRO 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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33A ILE 5.5 0.2 - - - -
34A SER* 4.7 4.3 - - - -
35A ARG 5.2 0.5 - - - +
37A GLY 4.7 0.2 - - - +
38A GLY* 1.3 86.4 - - - +
40A TRP* 1.3 68.4 + - - +
75A ARG* 3.8 41.3 - - - +
138A TRP* 5.3 2.7 - - + +
148A THR* 3.8 32.3 - - + +
193A GLY* 5.9 1.1 - - - -
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Residues in contact with TRP 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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33A ILE* 3.3 14.0 + - + +
34A SER 4.1 0.2 - - - -
35A ARG* 3.3 55.2 - - + +
39A PRO* 1.3 82.8 - - - +
41A CYS* 1.3 87.1 + - + +
57A CYS* 2.9 22.2 + - + -
61A TYR* 3.7 21.3 - + - -
66A PHE* 3.6 21.9 - + - -
193A GLY* 3.5 24.2 + - - -
195A SEB 3.8 30.0 - + - -
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Residues in contact with CYS 41 (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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32A SER* 3.8 3.5 - - - -
33A ILE* 2.8 38.0 + - + +
40A TRP* 1.3 92.4 + - + +
42A GLY* 1.3 64.1 + - - +
53A THR* 4.4 0.7 - - - +
57A CYS* 2.1 51.6 - - + -
138A TRP* 5.0 3.5 - - - -
193A GLY 3.6 10.9 + - - -
195A SEB 3.4 26.2 - - - -
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Residues in contact with GLY 42 (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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30A ILE* 5.8 0.2 - - - -
31A VAL 3.4 10.8 - - - -
32A SER* 4.6 0.7 - - - -
33A ILE* 3.5 8.4 - - - +
41A CYS* 1.3 74.2 - - - +
43A GLY* 1.4 57.0 + - - -
53A THR* 2.8 22.7 + - - -
137A GLY* 6.2 2.5 - - - -
138A TRP* 5.0 7.2 - - - -
193A GLY 4.0 3.4 + - - -
194A ASP 4.3 1.7 + - - -
195A SEB 2.9 8.1 + - - +
196A GLY* 3.1 6.1 - - - -
197A GLY* 3.5 16.6 - - - -
198A PRO* 5.6 0.2 - - - -
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Residues in contact with GLY 43 (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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30A ILE* 3.6 10.4 - - - +
31A VAL* 2.9 41.5 + - - +
33A ILE* 4.4 0.2 - - - -
42A GLY* 1.4 73.6 - - - -
44A SER* 1.3 63.7 + - - -
51A VAL* 4.2 4.3 - - - -
52A LEU 3.3 12.8 - - - -
53A THR* 4.3 0.9 - - - -
196A GLY 3.4 6.7 - - - -
197A GLY* 3.7 3.0 - - - -
198A PRO* 3.9 2.4 - - - +
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Residues in contact with SER 44 (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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29A PHE* 3.6 19.7 - - - -
43A GLY* 1.3 76.9 + - - -
45A LEU* 1.3 62.3 - - - +
46A LEU* 3.4 2.1 + - - +
51A VAL* 3.3 5.7 - - - +
52A LEU* 2.8 45.5 + - - +
118A ALA* 4.6 2.7 - - - -
196A GLY 4.9 0.7 + - - -
197A GLY 4.7 0.7 - - - -
198A PRO* 3.5 26.9 - - - +
206A LEU* 3.8 22.9 - - - +
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Residues in contact with LEU 45 (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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29A PHE* 2.8 23.8 + - - +
31A VAL* 4.2 7.3 - - + +
43A GLY 4.3 0.2 - - - -
44A SER* 1.3 70.4 - - - +
46A LEU* 1.3 57.5 + - - +
47A ASN 3.5 19.5 - - - +
50A THR 3.6 9.0 - - - +
51A VAL* 3.8 16.2 - - + -
70A ALA* 4.6 6.3 - - + -
105A LEU* 4.2 14.6 - - + -
109A ILE* 3.8 22.4 - - + -
115A ILE* 3.7 22.9 - - + -
116A GLY 4.0 3.6 - - - +
117A TYR* 3.4 27.8 - - + -
118A ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 46 (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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44A SER* 4.0 11.2 - - - +
45A LEU* 1.3 75.2 - - - +
47A ASN* 1.3 71.9 + - - +
50A THR* 2.8 14.9 + - + +
52A LEU* 4.0 22.4 - - + +
102A ILE* 3.9 21.5 - - + -
117A TYR* 3.5 15.2 - - - +
118A ALA* 4.2 16.7 - - + +
120A LEU* 4.0 27.8 - - + -
235A ILE* 3.9 26.2 - - + -
239A ALA* 3.9 12.6 - - + -
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Residues in contact with ASN 47 (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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45A LEU* 3.5 12.5 - - - +
46A LEU* 1.3 79.7 + - - +
48A ALA* 1.3 65.6 + - - +
49A ASN* 2.7 28.4 + - - +
50A THR* 2.7 25.8 + - - +
117A TYR* 3.5 21.3 - - + -
239A ALA* 2.8 35.6 + - - +
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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