Contacts of the strand formed by residues 49 - 57 (chain C) 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 MET 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B MET* 5.6 1.3 - - + +
90B ALA* 4.1 6.7 - - + -
92B LEU* 3.7 33.4 - - + -
44C TYR* 4.0 16.8 - - + +
45C VAL* 3.4 0.3 - - - +
46C LYS* 2.8 37.5 + - + +
47C THR* 6.1 0.2 - - - -
48C GLY* 1.3 82.5 - - - +
50C VAL* 1.3 77.0 + - - +
51C LEU* 4.8 6.7 - - + +
84C PHE* 3.3 5.1 - - - -
90C ALA* 3.4 19.1 - - + -
92C LEU* 5.1 11.4 - - + -
51D LEU* 3.9 28.9 - - + -
94D ALA* 4.0 20.0 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.6 20.0 - - + -
43C THR* 4.0 12.6 - - + -
44C TYR 3.5 4.9 - - - -
45C VAL* 3.7 10.8 - - + -
49C MET* 1.3 83.9 - - - +
51C LEU* 1.3 57.1 + - - +
52C VAL* 4.1 6.5 - - + -
68C THR* 3.5 29.8 - - + -
72C VAL* 4.8 2.2 - - + -
84C PHE* 3.4 23.8 - - + -
89C CYS* 4.3 5.2 - - - -
90C ALA 3.0 11.4 + - - +
91C VAL* 3.5 2.0 - - + +
92C LEU* 2.7 34.6 + - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.7 5.4 - - + -
42C GLU 3.7 1.4 - - - +
43C THR* 3.0 7.9 - - - +
44C TYR* 2.6 49.5 + - + +
49C MET* 4.8 6.5 - - + +
50C VAL* 1.3 71.9 - - - +
52C VAL* 1.3 69.0 + - - +
53C GLY 3.9 1.1 - - - +
92C LEU* 3.8 27.1 - - + +
93C SER 4.2 2.7 - - - +
94C ALA* 4.3 19.3 - - + +
44D TYR* 3.7 29.9 + - + -
49D MET* 4.0 10.3 - - + -
51D LEU* 3.5 30.3 - - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.2 8.7 - - + -
26C VAL* 4.3 11.7 - - + -
41C CYS* 3.4 30.1 - - - -
42C GLU 3.9 1.8 - - - -
43C THR* 4.2 5.4 - - + +
50C VAL* 4.1 15.3 - - + +
51C LEU* 1.3 75.2 - - - +
53C GLY* 1.3 57.4 + - - +
64C ILE* 3.6 31.9 - - + -
68C THR* 3.9 12.1 - - - +
91C VAL* 4.9 2.0 - - + -
92C LEU 2.9 12.5 + - - +
93C SER* 3.1 6.2 - - - -
94C ALA 3.0 19.7 + - - -
95C ILE* 3.3 13.3 - - + +
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Residues in contact with GLY 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C CYS* 3.3 11.3 - - - +
42C GLU 2.8 35.2 + - - -
52C VAL* 1.3 75.4 - - - +
54C GLY* 1.3 56.9 + - - -
56C ILE* 5.8 0.2 - - - +
94C ALA* 3.2 19.5 - - - -
95C ILE* 3.7 7.3 - - - +
44D TYR* 3.2 17.9 + - - -
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Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA 3.5 6.5 - - - -
42C GLU 4.5 1.1 - - - -
53C GLY* 1.3 74.4 - - - -
55C GLU* 1.3 75.7 + - - +
56C ILE 4.3 0.2 - - - -
94C ALA 3.2 6.3 + - - +
95C ILE* 3.4 3.2 - - - -
96C GLY 2.8 24.4 + - - -
44D TYR* 4.0 2.8 + - - -
46D LYS* 3.6 10.9 + - - +
239D CYS* 4.1 15.9 - - - -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG 4.0 2.3 - - - +
40C ALA* 2.9 39.0 + - + +
54C GLY* 1.3 75.7 - - - -
56C ILE* 1.3 62.3 + - - +
57C THR 4.3 0.2 - - - -
96C GLY 3.2 4.3 - - - -
97C LYS 3.7 24.7 - - - +
98C GLN* 3.7 5.2 - - - +
885C SAM 3.0 43.7 + - - +
46D LYS* 2.9 29.5 + - - +
236D MET 4.6 0.6 - - - +
237D GLY 4.0 12.1 - - - +
238D ASP* 3.2 12.6 + - - +
239D CYS* 3.3 10.5 + - - +
886D K 4.1 3.1 - - - -
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Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.1 15.5 - - + -
30C ILE* 3.6 26.2 - - + -
38C ARG 3.5 3.1 - - - -
39C VAL* 4.1 24.0 - - + -
40C ALA 4.3 0.9 - - - +
41C CYS* 4.4 10.8 - - + -
53C GLY 5.8 0.2 - - - +
55C GLU* 1.3 81.7 - - - +
57C THR* 1.3 65.4 + - - +
58C THR* 3.6 26.6 + - + -
64C ILE* 5.8 1.6 - - + -
95C ILE* 3.7 29.9 - - + +
96C GLY 2.6 17.4 + - - +
97C LYS* 3.3 14.0 - - - +
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Residues in contact with THR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA* 4.1 1.6 - - - -
38C ARG* 3.0 37.1 + - + +
56C ILE* 1.3 69.8 - - - +
58C THR* 1.3 61.5 + - - +
97C LYS* 3.4 16.8 - - + +
98C GLN* 2.8 42.1 + - - +
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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