Contacts of the strand formed by residues 15 - 24 (chain A) in PDB entry 5TA4
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 GLU 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ALA* 3.2 1.5 - - - -
12A VAL* 2.7 44.4 + - + +
13A ASP 3.4 3.5 - - - +
14A GLY* 1.3 80.7 - - - +
16A PRO* 1.3 78.6 - - - +
17A LEU* 3.3 0.3 + - - -
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Residues in contact with PRO 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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10A ILE 3.9 5.8 - - - +
11A ALA* 4.2 5.4 - - + -
14A GLY 3.3 9.4 - - - +
15A GLU* 1.3 95.4 - - + +
17A LEU* 1.3 61.3 + - - +
18A GLY* 5.1 1.3 - - - +
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Residues in contact with LEU 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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10A ILE* 2.8 19.8 + - + +
12A VAL* 4.0 27.8 - - + -
15A GLU 3.3 0.2 + - - -
16A PRO* 1.3 75.4 - - - +
18A GLY* 1.3 60.0 + - - +
138A ILE* 3.4 34.8 - - + +
141A ALA* 3.9 22.9 - - + -
142A MET* 3.8 30.7 - - + +
145A PHE* 5.2 3.8 - - + -
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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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8A PHE 3.9 0.2 - - - +
9A ASP* 3.7 3.8 - - - -
10A ILE* 2.9 32.4 + - - +
16A PRO* 3.9 1.8 - - - +
17A LEU* 1.3 82.7 - - - +
19A ARG* 1.3 61.3 + - - -
138A ILE* 3.8 14.1 - - - -
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Residues in contact with ARG 19 (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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7A PHE* 3.5 31.7 - - + -
8A PHE 3.3 9.0 - - - +
9A ASP* 2.8 39.3 + - - +
18A GLY* 1.3 72.5 - - - -
20A VAL* 1.3 72.2 + - - +
21A SER* 4.3 3.5 + - - +
134A GLU* 4.0 2.3 - - - +
135A GLY* 3.6 18.0 + - - -
138A ILE* 3.9 4.3 - - - +
160A ASP* 5.6 0.4 + - - -
164A LEU* 3.9 27.5 - - - +
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Residues in contact with VAL 20 (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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7A PHE* 3.2 3.1 - - - +
8A PHE* 2.8 36.3 + - + +
10A ILE* 4.3 12.1 - - + -
19A ARG* 1.3 74.5 - - - +
21A SER* 1.3 63.9 + - - +
22A PHE* 3.6 35.1 - - + -
114A ILE* 6.0 0.7 - - + -
132A VAL* 4.1 6.1 - - + -
134A GLU 3.5 9.9 - - - +
135A GLY 3.7 5.2 - - - +
138A ILE* 3.7 33.4 - - + -
139A VAL* 3.9 23.3 - - + -
142A MET* 5.1 1.3 - - - -
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Residues in contact with SER 21 (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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5A THR* 4.2 5.4 - - - -
6A VAL 3.2 10.1 - - - -
7A PHE* 4.6 2.2 - - - -
19A ARG* 4.2 4.0 - - - +
20A VAL* 1.3 76.0 - - - +
22A PHE* 1.3 59.6 + - - +
132A VAL* 3.4 7.1 - - - +
133A LYS* 2.7 35.8 + - - +
134A GLU* 2.9 40.1 + - - +
164A LEU* 4.1 20.9 - - - -
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Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PRO 3.7 0.3 - - - +
5A THR* 3.2 10.4 - - - -
6A VAL* 2.8 59.1 + - + +
8A PHE* 3.6 40.8 - + - -
20A VAL* 3.6 30.7 - - + -
21A SER* 1.3 78.6 - - - +
23A GLU* 1.3 60.0 + - - +
24A LEU* 3.8 11.3 + - + -
36A PHE* 4.4 4.3 - + - -
98A LEU* 4.0 20.9 - - + -
114A ILE* 3.7 33.7 - - + -
131A LYS 3.3 7.4 - - - +
132A VAL* 3.8 19.1 - - + -
133A LYS* 4.6 1.1 - - - -
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Residues in contact with GLU 23 (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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3A ASN* 3.0 37.6 + - + +
4A PRO 3.6 5.6 - - - +
5A THR* 4.7 6.1 - - - +
22A PHE* 1.3 72.2 - - - +
24A LEU* 1.3 63.2 + - - +
25A PHE* 3.5 17.7 - - + -
130A GLY* 3.1 4.3 - - - -
131A LYS* 2.8 60.1 + - + +
133A LYS* 4.3 15.1 - - + +
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Residues in contact with LEU 24 (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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3A ASN* 3.1 18.2 - - - +
4A PRO* 3.0 25.3 + - + +
6A VAL* 4.0 19.7 - - + -
22A PHE* 4.2 2.2 - - + +
23A GLU* 1.3 76.6 - - - +
25A PHE* 1.3 62.2 + - - +
26A ALA 2.8 9.0 + - - -
33A ALA* 3.6 33.9 - - + +
36A PHE* 3.6 26.2 - - + -
37A ARG* 3.8 28.3 - - + +
98A LEU* 3.9 19.3 - - + -
129A PHE* 3.6 9.2 - - + +
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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