Contacts of the strand formed by residues 53 - 62 (chain A) in PDB entry 3HSJ
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE 4.6 0.4 - - - -
8A GLY* 2.6 28.4 + - - -
9A SER* 3.2 32.3 - - - -
10A ASN* 3.7 10.5 - - + +
40A TYR 3.5 0.5 - - - +
41A ARG* 3.6 1.0 - - - -
42A THR* 2.7 55.2 + - - +
44A PRO* 6.5 0.4 - - + -
51A PRO 3.6 2.8 + - - +
52A ASP* 1.3 71.9 - - - +
54A LEU* 1.3 82.2 + - - +
55A ALA* 4.2 8.3 - - + -
92A ARG 6.0 0.4 - - - -
95A ASP* 3.6 22.8 + - - +
123A PHE* 4.3 10.6 - + - -
158A TRP* 3.8 1.8 - - - -
194A GOL 3.1 56.1 - - - +
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Residues in contact with LEU 54 (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 ILE* 4.9 2.5 - - + +
8A GLY* 3.1 7.3 - - - -
9A SER 3.0 30.0 + - - +
14A PRO* 4.1 19.5 - - + -
15A LEU* 3.5 32.3 - - + -
18A VAL* 3.7 36.3 - - + -
39A PHE* 4.2 17.5 - - + -
40A TYR 3.3 9.9 - - - +
52A ASP 3.9 0.4 + - - -
53A TYR* 1.3 75.3 - - - +
55A ALA* 1.3 73.1 + - - +
56A ALA* 4.4 2.5 - - + +
158A TRP* 3.6 26.8 - - + -
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Residues in contact with ALA 55 (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 ILE 3.4 7.2 - - - +
39A PHE* 3.8 0.3 - - - -
40A TYR* 2.8 43.1 + - + +
42A THR* 3.6 20.2 - - - +
53A TYR* 3.7 2.6 + - + -
54A LEU* 1.3 77.2 - - - +
56A ALA* 1.3 62.1 + - - +
123A PHE* 3.6 34.1 - - + +
127A PRO* 4.6 0.7 - - - -
155A LEU* 4.7 0.2 - - + -
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Residues in contact with ALA 56 (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 ALA* 3.5 5.9 - - - +
7A ILE* 2.9 39.8 + - + +
18A VAL* 5.6 0.2 - - + -
36A VAL* 4.9 3.4 - - + -
37A SER* 3.4 15.5 - - - +
38A SER 3.7 7.0 - - - +
39A PHE* 3.8 23.3 - - + -
54A LEU* 4.6 3.4 - - + -
55A ALA* 1.3 77.8 - - - +
57A ALA* 1.3 63.8 + - - +
123A PHE 5.4 0.9 - - - +
127A PRO* 4.0 8.1 - - - -
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Residues in contact with ALA 57 (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 3.4 5.2 - - - -
36A VAL* 3.5 3.6 - - - +
37A SER* 2.8 32.3 + - - -
56A ALA* 1.3 75.0 - - - +
58A VAL* 1.3 63.3 - - - +
99A MET* 4.1 17.0 - - + -
124A MET 5.1 0.7 - - - +
127A PRO* 3.8 6.7 - - + +
128A LEU* 3.8 29.6 - - + +
131A ILE* 3.8 13.8 - - + +
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Residues in contact with VAL 58 (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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3A ALA 3.5 1.0 - - - +
4A TYR* 3.3 5.2 - - - -
5A ILE* 2.8 43.8 + - + +
7A ILE* 3.5 33.9 - - + -
22A LEU* 3.5 14.6 - - + -
25A LEU* 4.1 8.5 - - + -
33A ILE* 4.1 24.9 - - + -
35A THR 3.6 8.1 - - - +
36A VAL* 4.2 6.1 - - + -
56A ALA 5.5 0.2 - - - -
57A ALA* 1.3 79.4 - - - +
59A ALA* 1.3 73.8 + - - +
60A LEU* 3.8 7.4 + - + +
131A ILE* 4.0 4.5 - - - -
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Residues in contact with ALA 59 (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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2A VAL* 4.3 4.9 - - + -
3A ALA 3.5 4.7 - - - -
4A TYR* 3.6 24.7 - - + -
33A ILE* 3.7 3.5 - - - -
34A LEU* 2.8 34.1 + - + -
35A THR* 2.9 22.6 + - + +
58A VAL* 1.3 73.2 - - - +
60A LEU* 1.3 54.8 + - - +
131A ILE* 3.8 2.5 - - + +
195A GOL 3.7 24.9 - - - -
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Residues in contact with LEU 60 (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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1A THR 3.4 1.0 - - - +
2A VAL* 3.5 2.3 - - - +
3A ALA* 2.8 43.6 + - + +
5A ILE* 4.0 20.4 - - + -
25A LEU* 3.8 24.2 - - + +
28A ILE* 4.5 5.8 - - + -
31A SER* 4.1 12.6 - - - +
32A HIS 3.5 26.9 - - - +
33A ILE* 3.9 12.6 - - + +
34A LEU* 4.6 1.3 - - - -
58A VAL* 3.8 3.8 + - + -
59A ALA* 1.3 72.9 - - - +
61A GLU* 1.3 65.8 + - - +
62A THR* 3.6 5.5 + - - -
69A LEU* 3.7 33.7 - - + -
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Residues in contact with GLU 61 (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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1A THR 2.8 31.1 + - - -
2A VAL* 3.7 18.7 - - - +
31A SER* 3.1 5.5 - - - -
32A HIS* 2.9 68.3 + - + +
34A LEU* 3.9 19.4 - - + +
60A LEU* 1.3 71.8 - - - +
62A THR* 1.3 60.5 + - - +
63A SER* 5.5 0.5 + - - -
192A ACT 4.0 8.8 - - + +
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Residues in contact with THR 62 (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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1A THR* 2.8 50.4 + - - +
3A ALA* 4.5 7.4 - - + -
30A GLU 3.4 4.0 - - - -
31A SER* 2.7 24.6 + - - -
60A LEU* 4.4 11.4 - - + +
61A GLU* 1.3 77.0 - - - +
63A SER* 1.3 58.1 + - - +
64A LEU* 3.0 24.5 + - + +
69A LEU* 4.5 6.2 - - + +
101A PHE* 3.9 30.7 - - + -
192A ACT 4.4 2.7 - - - -
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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