Contacts of the strand formed by residues 38 - 46 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 3.0 34.7 + - - +
37B ALA* 1.3 78.7 + - - +
39B VAL* 1.3 60.1 + - - +
40B ALA 4.2 0.2 - - - -
55B GLU 4.0 1.8 - - - +
56B ILE* 3.4 3.6 - - - -
57B THR* 2.9 48.1 + - - +
98B GLN* 4.1 35.5 - - + +
103B ASN* 4.3 2.0 - - - +
106B VAL* 3.5 9.9 - - + +
107B ASP* 2.4 43.8 + - - +
266B ASP* 3.1 9.5 + - - +
268B SER* 3.4 22.0 + - - +
269B LYS* 4.7 2.0 - - - +
338B TYR* 3.1 26.4 + - - -
341B ILE* 6.0 1.4 - - - +
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Residues in contact with VAL 39 (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 VAL* 5.1 0.2 - - + -
27B LEU* 3.4 39.5 - - + +
30B ILE* 3.9 36.3 - - + -
37B ALA* 4.4 6.5 - - + -
38B ARG* 1.3 76.4 - - - +
40B ALA* 1.3 61.3 + - - +
41B CYS* 4.0 15.9 - - + -
55B GLU 4.2 1.3 - - - -
56B ILE* 4.0 14.1 - - + -
264B GLY 2.9 23.9 - - - +
265B LYS* 3.0 17.3 - - - -
266B ASP* 2.7 12.7 + - - -
269B LYS* 3.3 5.7 - - - -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ANP 6.1 0.2 - - - +
39B VAL* 1.3 73.2 - - - +
41B CYS* 1.3 59.4 + - - +
42B GLU* 3.9 5.7 + - + +
54B GLY* 3.4 5.2 - - - -
55B GLU* 3.0 43.7 + - + +
56B ILE* 4.9 0.2 - - - -
264B GLY 3.4 3.4 - - - -
265B LYS* 4.7 5.6 - - + +
269B LYS* 4.2 7.6 - - - +
385B MET* 3.3 37.2 - - + +
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Residues in contact with CYS 41 (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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23B SER* 3.0 37.4 + - - +
26B VAL* 4.3 10.3 - - + -
39B VAL* 4.0 13.0 - - + -
40B ALA* 1.3 72.2 - - - +
42B GLU* 1.3 66.4 + - - +
43B THR* 4.1 0.9 - - - -
52B VAL* 3.4 33.7 - - - -
53B GLY 3.4 7.0 - - - +
56B ILE* 4.4 10.5 - - + -
95B ILE* 5.8 0.2 - - - -
263B SER 4.3 0.7 - - - +
264B GLY* 2.8 30.0 + - - +
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Residues in contact with GLU 42 (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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44A TYR* 3.0 19.0 + - - +
239A CYS* 4.0 19.9 - - + +
241A LEU* 4.0 12.5 - - + +
244A ARG* 2.8 44.6 + - - -
384A ANP 4.4 0.3 + - - -
386A K 3.2 23.8 - - - -
40B ALA 3.9 7.4 + - - +
41B CYS* 1.3 76.9 - - - +
43B THR* 1.3 61.6 + - - +
51B LEU 3.7 0.2 - - - +
53B GLY 2.7 37.6 + - - +
242B THR* 3.3 17.3 - - - +
263B SER 5.0 1.3 - - - +
265B LYS* 5.2 1.4 + - - -
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Residues in contact with THR 43 (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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44A TYR* 4.6 0.7 - - - -
19B ALA* 3.7 9.9 - - - +
22B ILE* 3.9 23.9 - - + +
23B SER* 2.8 24.4 + - - -
41B CYS* 4.1 0.2 - - - -
42B GLU* 1.3 76.4 + - - +
44B TYR* 1.3 60.4 + - - +
45B VAL* 4.0 18.2 - - + -
50B VAL* 4.0 6.3 - - + -
51B LEU 3.0 18.8 - - - +
52B VAL* 4.1 8.4 - - + +
241B LEU* 3.3 8.4 - - - +
242B THR* 2.8 41.2 + - - -
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Residues in contact with TYR 44 (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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42A GLU 2.9 27.7 + - - -
44A TYR* 3.6 36.1 - + + -
51A LEU* 3.9 23.1 - - + -
52A VAL 4.5 0.2 - - - -
53A GLY* 3.4 19.8 + - - -
94A ALA* 5.4 1.3 - - + -
42B GLU 4.3 0.2 + - - -
43B THR* 1.3 72.3 - - - +
45B VAL* 1.3 66.4 + - - +
46B LYS* 4.6 6.3 - - + -
49B MET* 4.0 19.5 - - + +
50B VAL* 3.5 0.5 - - - -
51B LEU* 2.6 53.5 + - + +
239B CYS* 3.6 28.0 - - - -
240B GLY 3.6 2.7 - - - -
241B LEU* 3.3 30.3 - - + -
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Residues in contact with VAL 45 (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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15B PRO 4.7 2.0 - - - +
18B ILE* 4.4 12.6 - - + -
19B ALA* 4.2 20.6 - - + +
22B ILE* 5.0 0.2 - - + -
43B THR* 4.0 17.7 - - + -
44B TYR* 1.3 82.7 - - - +
46B LYS* 1.3 65.7 + - - +
49B MET 3.4 14.4 - - - +
50B VAL* 3.7 17.9 - - + -
84B PHE* 3.8 3.1 - - + -
235B PRO* 3.6 25.2 - - + +
239B CYS* 3.7 2.6 - - - -
240B GLY* 2.7 49.3 + - - +
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Residues in contact with LYS 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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54A GLY 4.0 11.2 + - - +
55A GLU* 2.7 33.2 + - - +
94A ALA* 4.4 19.3 - - + +
96A GLY* 4.8 8.2 - - - +
97A LYS 5.3 1.4 + - - -
44B TYR* 4.6 5.1 - - + -
45B VAL* 1.3 72.3 - - - +
47B THR* 1.3 77.4 + - + +
48B GLY 2.8 17.8 + - - -
49B MET* 2.9 42.1 + - + +
84B PHE* 3.0 4.5 - - - -
235B PRO* 3.1 26.9 - - - -
236B MET 3.5 17.4 + - - -
239B CYS* 3.7 30.3 - - + +
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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