Contacts of the strand formed by residues 32 - 41 (chain A) in PDB entry 1TD2
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 ASN 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A MET* 3.9 22.7 - - - +
3A LYS 2.8 8.2 + - - +
4A ASN* 3.2 28.6 - - - +
5A ILE* 3.1 24.6 + - - +
27A ARG* 4.8 0.7 - - - -
31A ALA* 1.3 76.0 - - - +
33A VAL* 1.3 66.0 + - - +
34A TRP* 4.5 9.9 - - + +
16B HIS* 4.3 16.5 + - - -
267B GLN* 4.8 8.1 + - - +
269B VAL* 3.6 29.5 - - - +
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Residues in contact with VAL 33 (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 ILE* 3.5 4.9 - - + +
7A ALA* 4.0 25.4 - - + -
19A ASN* 4.9 1.3 - - - +
23A GLU* 4.2 15.0 - - + +
26A MET* 3.7 42.0 - - + -
27A ARG* 2.8 52.7 + - + +
31A ALA 4.5 1.8 - - - +
32A ASN* 1.3 80.4 - - - +
34A TRP* 1.3 71.5 + - - +
35A PRO* 3.3 12.2 - - + +
13B VAL 4.5 0.3 - - - +
16B HIS* 5.6 0.3 - - - -
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Residues in contact with TRP 34 (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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4A ASN* 3.6 31.2 + - + +
5A ILE 2.8 14.3 + - - +
6A LEU* 3.6 32.0 - - + +
7A ALA 3.2 19.4 + - - -
32A ASN* 4.5 5.8 - - + +
33A VAL* 1.3 83.6 - - - +
35A PRO* 1.3 65.7 - - - +
36A LEU 3.2 2.3 + - - -
67A ILE* 4.3 24.9 - - + -
72A LYS 3.8 5.6 - - - -
73A LEU* 4.7 5.4 - - + -
75A THR* 3.3 28.0 - - - -
76A CYS* 3.5 31.2 - - + -
13B VAL* 3.1 20.4 - - + +
14B TYR* 3.6 29.9 - + - -
15B GLY 5.0 3.1 - - - +
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Residues in contact with PRO 35 (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 ALA 3.7 4.9 - - - +
19A ASN* 3.7 23.3 - - + +
23A GLU* 4.8 8.1 - - + -
27A ARG* 4.0 16.2 - - - +
33A VAL* 3.3 21.3 - - + +
34A TRP* 1.3 80.1 - - - +
36A LEU* 1.3 59.4 + - - +
37A ASN* 3.4 9.3 + - - +
11B HIS* 2.9 48.5 - - + +
12B VAL 4.4 1.8 - - - +
13B VAL* 3.4 17.3 - - - +
20B SER* 6.2 0.4 - - - -
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Residues in contact with LEU 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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6A LEU* 4.2 4.5 - - + -
7A ALA 3.1 7.2 + - - -
8A ILE* 3.3 59.6 - - + +
9A GLN 3.5 0.9 + - - -
34A TRP 3.2 2.0 + - - -
35A PRO* 1.3 70.4 - - - +
37A ASN* 1.3 64.0 + - - +
38A THR 3.4 0.7 + - - -
59A HIS* 4.6 0.2 - - + -
60A LEU* 3.6 37.2 - - + +
63A ILE* 3.8 33.2 - - + -
64A VAL* 3.9 17.5 - - + -
96A ILE* 4.0 8.5 - - + -
13B VAL* 3.9 13.2 - - + -
40B GLN* 4.2 8.3 - - - +
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Residues in contact with ASN 37 (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 GLN 3.2 4.0 - - - -
11A HIS* 3.4 37.2 + - + +
19A ASN* 2.7 40.6 - - - +
35A PRO* 3.7 12.1 - - - +
36A LEU* 1.3 69.9 - - - +
38A THR* 1.3 59.8 + - - +
39A VAL 3.7 6.7 - - - +
40A GLN* 6.0 0.2 - - + -
55A MET* 3.0 25.0 - - + +
60A LEU* 4.2 3.5 - - - +
11B HIS* 3.7 12.0 + - - -
37B ASN* 3.8 8.8 - - - +
40B GLN* 3.1 27.6 + - - +
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Residues in contact with THR 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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8A ILE* 3.4 33.4 - - + +
9A GLN* 2.9 24.7 + - - +
10A SER* 3.1 4.3 + - - -
37A ASN* 1.3 72.3 - - - +
39A VAL* 1.3 69.4 + - - +
55A MET* 2.9 21.3 + - - -
60A LEU* 4.3 6.1 - - + -
83A TYR 2.9 21.7 + - - +
84A LEU* 4.3 4.3 - - + -
85A GLY 4.1 3.6 + - - -
89A GLN* 3.1 36.7 - - - +
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Residues in contact with VAL 39 (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 SER* 3.8 24.4 - - - +
11A HIS* 3.3 25.4 + - - +
37A ASN* 3.2 6.9 - - - +
38A THR* 1.3 91.9 + - - +
40A GLN* 1.3 59.6 + - - +
41A PHE* 3.6 34.3 - - + -
53A CYS 3.1 13.0 - - - +
54A VAL* 3.7 17.7 - - + -
55A MET* 3.4 10.8 - - - -
83A TYR* 4.6 3.8 - - + -
85A GLY* 3.8 21.8 - - - -
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Residues in contact with GLN 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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11A HIS* 3.4 21.3 + - + -
13A VAL* 4.0 12.1 - - + -
37A ASN* 6.0 0.2 - - + -
39A VAL* 1.3 72.6 - - - +
41A PHE* 1.3 59.6 + - - +
52A GLY* 3.2 6.4 - - - -
53A CYS 2.9 29.1 + - - -
55A MET* 3.3 16.2 - - + +
35B PRO 4.0 0.2 + - - -
36B LEU* 3.7 8.5 - - - +
37B ASN* 3.1 61.6 + - - +
55B MET* 4.0 5.2 - - - +
59B HIS* 2.8 32.9 + - + +
63B ILE* 3.8 0.8 - - + +
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Residues in contact with PHE 41 (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 10.9 + - - +
12A VAL* 3.1 6.2 - - + -
13A VAL* 2.8 33.8 + - - +
39A VAL* 3.6 27.6 - - + -
40A GLN* 1.3 81.7 - - - +
42A SER* 1.3 56.3 + - - +
43A ASN 3.4 15.7 - - - +
45A THR* 4.3 4.7 - - + -
50A TRP* 3.5 33.0 - + + -
51A THR 3.2 11.4 - - - +
52A GLY 4.2 2.2 - - - -
53A CYS* 3.4 30.3 - - - -
54A VAL* 4.3 10.1 - - + -
83A TYR* 4.0 20.9 - - - -
85A GLY* 6.1 0.2 - - - -
288A PXL 4.0 14.1 - - + -
63B ILE* 3.7 4.0 - - - -
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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