Contacts of the strand formed by residues 10 - 18 (chain A) in PDB entry 1EFU
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 PRO 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS* 1.3 86.1 - - + +
11A HIS* 1.3 62.4 + - - +
73A THR 3.5 14.4 - - - +
74A ARG* 3.4 17.0 - - + +
75A HIS 2.8 28.6 + - - +
201A GLU* 3.6 44.2 - - + +
202A PRO* 5.1 3.8 - - + -
204A ARG* 6.4 1.3 - - - -
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Residues in contact with HIS 11 (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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9A LYS 3.4 4.5 + - - +
10A PRO* 1.3 72.7 - - - +
12A VAL* 1.3 63.1 + - - +
13A ASN* 3.0 42.4 + - - -
68A GLU* 5.4 1.6 + - - -
75A HIS* 3.3 33.6 + + + -
77A ALA* 3.4 18.4 - - + +
99A ASP* 4.3 1.4 - - - +
202A PRO* 3.1 23.8 - - - +
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Residues in contact with VAL 12 (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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10A PRO 4.6 0.7 - - - +
11A HIS* 1.3 81.6 + - - +
13A ASN* 1.3 65.4 + - - +
14A VAL* 4.0 10.3 + - + -
74A ARG* 3.8 34.5 - - + +
75A HIS 2.8 7.6 + - - +
76A TYR* 3.2 28.9 - - + -
77A ALA 2.8 26.0 + - - -
99A ASP* 3.5 21.3 - - + +
199A ILE* 4.1 12.3 - - + -
200A PRO 5.1 0.2 - - - +
202A PRO* 3.8 19.3 - - + -
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Residues in contact with ASN 13 (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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11A HIS* 3.0 35.1 + - - +
12A VAL* 1.3 71.4 - - - +
14A VAL* 1.3 61.8 + - - +
77A ALA* 3.2 16.9 + - - +
79A VAL* 6.3 0.6 - - - +
97A GLN 3.9 23.5 - - - +
98A MET* 3.7 4.0 - - + -
99A ASP* 2.8 49.5 + - - +
100A GLY 3.4 2.9 + - - -
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Residues in contact with VAL 14 (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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12A VAL* 4.0 8.3 - - + -
13A ASN* 1.3 80.3 - - - +
15A GLY* 1.3 59.9 + - - +
69A TYR* 3.1 30.5 - - + +
76A TYR* 3.9 23.8 - - + -
77A ALA 2.8 13.4 + - - +
78A HIS* 3.2 18.0 - - + +
79A VAL* 2.9 26.5 + - - +
98A MET* 4.3 4.5 - - - -
100A GLY 3.3 12.1 - - - +
102A ILE* 5.0 7.6 - - + -
195A LEU* 4.2 9.6 - - + -
199A ILE* 4.2 15.3 - - + -
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Residues in contact with GLY 15 (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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14A VAL* 1.3 79.2 - - - +
16A THR* 1.3 63.0 + - - -
78A HIS* 4.4 3.4 - - - -
79A VAL* 2.9 15.7 - - - -
81A CYS* 4.5 0.7 - - - -
98A MET* 3.7 20.7 - - - -
100A GLY 3.4 6.7 + - - -
101A ALA* 3.5 4.7 - - - +
102A ILE* 2.9 27.0 + - - +
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Residues in contact with THR 16 (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 GLY* 1.3 73.7 - - - +
17A ILE* 1.3 61.6 + - - +
24A LYS* 3.7 14.5 + - - +
27A LEU* 4.6 5.4 - - + -
28A THR* 4.1 5.9 + - - +
78A HIS* 3.0 34.5 + - + +
79A VAL 3.0 5.3 + - - -
80A ASP* 2.6 28.7 + - - +
81A CYS* 2.9 27.1 + - - -
102A ILE* 3.5 18.4 - - + +
104A VAL* 4.1 15.3 - - + -
271B PHE* 3.9 4.3 - - - -
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Residues in contact with ILE 17 (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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16A THR* 1.3 75.8 - - - +
18A GLY* 1.3 60.3 + - - +
24A LYS* 3.6 6.7 - - - +
81A CYS* 4.2 18.6 - - + +
98A MET* 6.2 2.9 - - + -
101A ALA* 4.7 15.0 - - + -
102A ILE 3.2 11.9 + - - +
103A LEU* 3.3 21.5 - - + +
104A VAL 3.2 20.8 + - - -
118A HIS* 3.4 47.6 - - + +
121A LEU* 3.9 13.2 - - + -
122A GLY* 5.2 2.2 - - - +
130A ILE* 5.9 4.7 - - + -
81B PHE* 3.7 16.8 - - + -
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Residues in contact with GLY 18 (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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17A ILE* 1.3 79.8 - - - +
19A HIS* 1.3 67.3 + - - +
20A VAL* 3.5 2.6 + - - +
24A LYS* 3.2 24.6 + - - +
81A CYS 5.2 0.2 + - - -
103A LEU* 4.6 1.3 - - - -
104A VAL 3.8 13.0 - - - -
118A HIS* 3.4 22.9 + - - -
81B PHE* 5.9 1.2 - - - -
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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