Contacts of the strand formed by residues 35 - 40 (chain A) in PDB entry 4TQ1
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 TYR 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A CYS* 3.6 0.3 - - - -
20A PHE* 2.7 46.7 + - + +
34A PRO* 1.3 76.0 - - - +
36A TYR* 1.3 64.9 + - - +
37A LEU* 3.5 32.8 - - + -
51A LYS* 3.5 34.1 - - + +
52A VAL* 4.0 15.7 - - + -
55A HIS* 3.5 45.5 - + + -
56A PHE* 4.3 6.7 - - + -
601B GLU* 3.2 23.7 + - - -
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Residues in contact with TYR 36 (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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18A THR 3.3 4.3 - - - -
19A CYS* 3.5 41.2 - - + -
34A PRO* 3.8 28.2 - - + +
35A TYR* 1.3 79.0 - - - +
37A LEU* 1.3 73.1 + - - +
97A PRO* 4.5 4.5 - - + -
600B TYR* 3.5 44.0 - + + -
601B GLU* 4.2 12.1 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO* 3.7 0.2 - - - +
18A THR* 2.9 35.3 + - - +
20A PHE* 4.3 4.0 - - + -
35A TYR* 3.5 27.7 + - + +
36A TYR* 1.3 80.0 - - - +
38A LEU* 1.3 60.3 + - - +
39A LEU* 3.6 16.6 + - + -
48A VAL 4.3 7.6 - - - +
51A LYS* 4.1 10.8 - - + -
52A VAL* 3.6 28.3 - - + -
600B TYR* 3.8 7.1 - - - -
601B GLU* 3.4 26.7 - - + +
602B GLN 4.0 10.8 - - - +
603B ALA* 3.8 22.0 - - + -
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Residues in contact with LEU 38 (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 ARG* 4.0 18.0 - - + -
16A ILE 3.9 1.6 - - - -
17A PRO* 3.9 32.1 - - + -
37A LEU* 1.3 70.5 - - - +
39A LEU* 1.3 61.7 + - - +
40A PRO* 3.9 2.3 - - - +
594B LEU* 4.1 22.9 - - + -
597B PHE* 3.8 23.3 - - + +
598B ARG* 4.9 4.3 - - - +
600B TYR* 3.6 26.9 - - + +
601B GLU 2.9 12.1 + - - +
602B GLN* 3.6 28.0 - - - +
603B ALA* 3.2 22.9 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.2 6.9 - - - -
16A ILE* 2.8 39.3 + - + +
18A THR* 3.3 32.8 - - + +
20A PHE* 3.8 24.7 - - + -
37A LEU* 4.1 9.0 - - + +
38A LEU* 1.3 70.4 - - - +
40A PRO* 1.3 68.3 - - + +
45A LEU* 3.8 27.8 - - + -
48A VAL* 4.2 11.4 - - + +
49A THR* 4.8 1.1 - - + -
83A ILE* 4.1 22.0 - - + -
98A TRP* 4.4 3.8 - - + -
603B ALA* 3.9 20.2 - - + -
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Residues in contact with PRO 40 (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 TRP 5.4 0.2 - - - +
14A GLY 3.5 7.9 - - - +
15A ARG* 3.6 24.7 - - - +
38A LEU 3.9 5.2 - - - +
39A LEU* 1.3 83.1 - - + +
41A ARG* 1.3 66.0 + - - +
42A VAL* 3.1 11.2 + - + +
43A SER* 3.3 19.7 + - - +
48A VAL* 4.1 29.8 - - + -
83A ILE* 3.4 16.9 - - - +
160A ASP* 5.1 6.3 - - - +
603B ALA* 4.2 5.4 - - + -
604B VAL* 4.4 13.2 - - + +
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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