Contacts of the strand formed by residues 5 - 15 (chain C) in PDB entry 1P27
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 PHE 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C SER 3.3 9.7 + - - +
4C ASP* 1.3 75.4 - - - +
6C TYR* 1.3 69.0 + - - +
7C LEU* 3.8 25.6 - - + -
26C PHE* 4.0 6.7 - - + -
28C PRO* 3.2 37.0 - - + +
54C LYS* 5.7 1.3 - - - +
57C MET* 3.3 32.5 - - + -
60C LEU* 3.9 24.2 - - + -
61C LYS* 3.6 37.2 - - + -
64C ILE* 3.6 27.8 - - + -
90C ILE* 4.8 0.7 - - + -
91C VAL* 3.3 18.1 - - - +
92C ILE* 3.7 9.2 - - + -
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Residues in contact with TYR 6 (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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27A ARG* 3.3 18.0 + - - -
5C PHE* 1.3 80.2 - - - +
7C LEU* 1.3 63.5 + - - +
8C ARG* 3.2 31.3 - - + -
25C GLU* 2.5 45.3 + - + -
26C PHE 3.6 13.9 - - - -
27C ARG* 4.4 4.9 - - + -
28C PRO* 4.3 14.8 - - + -
89C GLU* 3.7 34.3 - - + -
90C ILE* 3.3 5.7 - - - +
91C VAL* 2.9 50.6 + - + +
96C HIS* 4.7 0.7 - + - -
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Residues in contact with LEU 7 (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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5C PHE* 3.8 17.5 - - + -
6C TYR* 1.3 78.7 - - - +
8C ARG* 1.3 71.2 + - - +
9C TYR* 4.8 0.2 - - + -
24C PHE* 3.8 28.0 - - + -
25C GLU* 3.2 4.7 - - - +
26C PHE* 2.8 48.3 + - + +
60C LEU* 4.9 1.3 - - + -
64C ILE* 3.7 26.5 - - + -
88C LEU* 4.3 2.9 - - + -
89C GLU 3.3 7.0 - - - +
90C ILE* 3.9 16.2 - - + -
129C LEU* 3.9 31.0 - - + -
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Residues in contact with ARG 8 (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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27A ARG* 4.3 0.2 - - - +
33A ARG* 3.0 37.0 - - - +
49A GLU* 4.1 6.5 + - - -
6C TYR* 3.2 27.0 + - + +
7C LEU* 1.3 79.2 - - - +
9C TYR* 1.3 64.9 + - - +
10C TYR* 4.0 6.5 - - - +
23C GLU* 3.1 27.5 + - + +
24C PHE 3.3 12.6 - - - +
25C GLU* 4.0 12.1 - - + -
87C GLU* 2.8 37.3 + - - +
88C LEU* 3.4 7.1 - - - +
89C GLU* 2.9 64.4 + - + +
98C SER* 5.6 1.0 + - - -
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Residues in contact with TYR 9 (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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7C LEU* 4.4 0.9 - - + +
8C ARG* 1.3 76.1 - - - +
10C TYR* 1.3 66.0 + - - +
11C VAL* 3.4 37.9 - - + +
22C LEU* 4.9 3.6 - - + -
23C GLU* 3.1 7.9 - - - +
24C PHE* 2.9 72.8 + + + -
86C GLN* 2.6 36.5 + - + -
87C GLU 3.3 15.0 - - - -
88C LEU* 4.5 12.8 - - + -
122C PHE* 4.6 1.3 - + - -
126C VAL* 3.5 38.0 - - + +
129C LEU* 5.2 2.2 - - + -
130C LYS* 4.5 11.5 + - + -
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Residues in contact with TYR 10 (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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45A MET* 3.4 16.1 - - + +
47A ARG* 3.5 44.9 - - - -
8C ARG* 4.0 1.8 - - - +
9C TYR* 1.3 77.6 - - - +
11C VAL* 1.3 65.4 + - - +
12C GLY* 3.4 20.9 - - - -
19C HIS* 3.4 29.1 + - - -
21C PHE* 3.8 22.2 - + + -
22C LEU 3.5 7.4 - - - -
23C GLU* 3.9 21.1 - - + +
85C ARG* 3.8 18.6 - - + -
86C GLN* 3.2 6.4 - - - +
87C GLU* 2.9 54.4 + - + +
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Residues in contact with VAL 11 (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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9C TYR* 3.4 30.5 - - + +
10C TYR* 1.3 77.2 - - - +
12C GLY* 1.3 67.0 + - - +
13C HIS* 5.6 2.9 - - + -
21C PHE* 3.0 5.5 - - - +
22C LEU* 2.9 57.9 + - + -
85C ARG 3.4 4.7 - - - +
86C GLN* 3.8 18.4 - - + +
103C LYS* 4.9 9.9 - - + -
130C LYS* 5.6 4.3 - - + +
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Residues in contact with GLY 12 (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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10C TYR* 3.4 24.0 - - - -
11C VAL* 1.3 79.8 - - - +
13C HIS* 1.3 63.0 + - - +
19C HIS* 4.0 4.7 - - - -
20C GLU 3.2 8.3 - - - -
21C PHE* 4.0 0.2 - - - -
84C GLY* 3.2 4.8 - - - -
85C ARG* 2.9 34.6 + - - +
103C LYS* 4.7 0.9 - - - +
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Residues in contact with HIS 13 (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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11C VAL* 5.6 3.4 - - + -
12C GLY* 1.3 76.3 - - - +
14C LYS* 1.3 75.0 + - - +
15C GLY* 3.4 9.0 + - - -
19C HIS* 3.4 5.4 - - - -
20C GLU* 2.8 65.8 + - + +
83C VAL* 3.2 20.1 - - + +
103C LYS* 4.0 29.3 - - + +
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Residues in contact with LYS 14 (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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42A ASN* 2.7 42.6 - - - +
43A ASP* 2.9 43.8 - - - +
44A VAL* 6.2 0.2 - - - -
13C HIS* 1.3 80.3 + - - +
15C GLY* 1.3 65.5 + - - +
18C GLY* 4.3 5.6 - - - +
19C HIS* 4.0 24.0 - - + +
82C ARG 3.3 25.6 - - - +
83C VAL* 3.0 20.5 + - + +
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Residues in contact with GLY 15 (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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13C HIS* 3.4 15.7 + - - -
14C LYS* 1.3 83.1 + - - +
16C LYS* 1.3 66.4 - - - +
17C PHE 3.2 3.7 + - - -
18C GLY* 3.0 25.1 + - - -
20C GLU* 4.5 8.0 + - - -
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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