Contacts of the strand formed by residues 38 - 46 (chain A) in PDB entry 1P7L
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 ARG 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LYS* 3.0 35.7 + - - +
37A ALA* 1.3 76.7 + - - +
39A VAL* 1.3 61.3 + - - +
40A ALA 4.2 0.2 - - - -
55A GLU 4.1 1.4 - - - +
56A ILE* 3.5 3.3 - - - -
57A THR* 3.0 42.5 + - - +
98A GLN* 4.1 35.7 - - - +
103A ASN* 4.3 2.6 - - - +
106A VAL* 3.5 11.1 - - + +
107A ASP* 2.4 42.9 + - - -
266A ASP* 3.1 10.2 + - - +
268A SER* 3.6 19.8 + - - +
269A LYS* 4.7 1.8 - - - +
338A TYR* 3.0 27.3 + - - -
341A ILE* 6.0 1.2 - - - +
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Residues in contact with VAL 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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26A VAL* 5.0 0.2 - - + -
27A LEU* 3.4 40.2 - - + +
30A ILE* 3.9 34.8 - - + -
31A LEU* 5.6 0.2 - - + -
37A ALA* 4.4 7.6 - - + -
38A ARG* 1.3 75.5 - - - +
40A ALA* 1.3 60.1 + - - +
41A CYS* 4.0 15.0 - - + -
55A GLU 4.2 1.3 - - - -
56A ILE* 4.1 13.9 - - + -
264A GLY 2.9 25.8 - - - +
265A LYS* 3.0 16.6 - - - -
266A ASP* 2.8 12.7 + - - -
269A LYS* 3.3 6.3 - - - -
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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 ARG 5.9 0.2 - - - -
39A VAL* 1.3 73.6 - - - +
41A CYS* 1.3 59.4 + - - +
42A GLU* 3.9 5.7 + - + +
54A GLY* 3.4 5.4 - - - -
55A GLU* 2.9 44.6 + - + +
56A ILE* 4.9 0.4 - - - -
264A GLY 3.5 2.9 - - - -
265A LYS* 4.7 5.6 - - + +
269A LYS* 4.2 6.5 - - - +
485A MET* 3.2 39.0 - - + +
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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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23A SER* 3.0 33.9 + - - +
26A VAL* 4.2 14.4 - - - -
39A VAL* 4.0 13.2 - - + -
40A ALA* 1.3 71.3 - - - +
42A GLU* 1.3 68.3 + - - +
43A THR* 4.3 0.2 - - - -
52A VAL* 3.4 32.3 - - - -
53A GLY 3.4 8.1 - - - -
56A ILE* 4.5 9.9 - - + -
95A ILE* 5.8 0.2 - - - -
263A SER 4.2 1.2 - - - +
264A GLY* 2.8 31.8 + - - +
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Residues in contact with GLU 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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40A ALA 3.9 6.5 + - - +
41A CYS* 1.3 75.3 - - - +
43A THR* 1.3 63.1 + - - +
51A LEU 3.7 0.2 - - - +
53A GLY 2.9 23.9 + - - +
242A THR* 3.4 17.0 - - - +
263A SER 5.0 1.4 - - - +
265A LYS* 5.2 1.9 + - - +
44B TYR* 2.9 30.8 + - - +
239B CYS* 4.0 21.1 - - + +
241B LEU* 4.1 12.2 - - + +
244B ARG* 2.9 42.6 + - - -
484B ANP 4.4 0.5 + - - -
486B K 3.2 25.2 - - - -
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Residues in contact with THR 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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19A ALA* 3.7 9.5 - - - +
22A ILE* 3.9 23.8 - - + +
23A SER* 2.7 29.0 + - - -
41A CYS* 4.3 0.2 - - - -
42A GLU* 1.3 75.3 + - - +
44A TYR* 1.3 59.4 + - - +
45A VAL* 4.0 12.1 - - + -
50A VAL* 3.9 12.8 - - + -
51A LEU 3.0 19.3 - - - +
52A VAL* 4.2 8.0 - - + +
241A LEU* 3.3 8.4 - - - +
242A THR* 2.7 41.4 + - - -
44B TYR* 4.6 0.7 - - - -
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Residues in contact with TYR 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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42A GLU 4.3 0.4 + - - -
43A THR* 1.3 71.7 - - - +
45A VAL* 1.3 66.8 + - - +
46A LYS* 4.5 6.1 - - + -
49A MET* 4.0 24.6 - - + +
50A VAL* 3.5 0.5 - - - -
51A LEU* 2.6 52.8 + - + +
239A CYS* 3.5 24.0 - - - -
240A GLY 3.7 2.5 - - - -
241A LEU* 3.3 34.1 - - + -
42B GLU 3.0 27.0 + - - -
44B TYR* 3.6 35.0 - + + -
51B LEU* 3.9 19.9 - - + +
53B GLY* 3.3 20.9 + - - -
94B ALA* 5.4 1.3 - - + -
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Residues in contact with VAL 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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15A PRO 4.7 2.5 - - - +
18A ILE* 4.4 11.7 - - + -
19A ALA* 4.2 21.3 - - + +
43A THR* 4.0 17.9 - - + -
44A TYR* 1.3 82.2 - - - +
46A LYS* 1.3 63.2 + - - +
49A MET 3.4 17.3 - - - +
50A VAL* 3.7 16.2 - - + -
84A PHE* 3.8 3.4 - - + -
235A PRO* 3.6 25.5 - - + +
239A CYS* 3.6 3.8 - - - -
240A GLY* 2.7 48.8 + - - +
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Residues in contact with LYS 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 TYR* 4.5 11.9 - - + -
45A VAL* 1.3 72.6 - - - +
47A THR* 1.3 95.4 + - + +
48A GLY 2.8 5.3 + - - -
49A MET* 2.9 34.2 + - + +
84A PHE* 3.0 4.3 - - - -
235A PRO* 3.2 27.4 - - - -
236A MET 3.6 11.9 + - - -
239A CYS* 3.7 29.6 - - + +
54B GLY 3.9 14.3 + - - +
55B GLU* 2.8 31.8 + - - +
94B ALA* 4.4 18.8 - - + +
96B GLY* 4.7 8.6 - - - +
97B LYS 5.4 1.4 + - - -
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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