Contacts of the strand formed by residues 94 - 102 (chain A) in PDB entry 2YD6
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 ALA 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LYS* 3.8 32.5 - - + +
60A LYS* 5.5 6.3 - - - -
92A ASP 3.3 3.2 + - - +
93A GLU* 1.3 76.3 - - - +
95A ILE* 1.3 65.9 + - - +
96A TYR* 3.6 18.1 - - + +
112A ARG* 3.6 8.3 - - - +
113A LEU 3.0 30.6 + - - +
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Residues in contact with ILE 95 (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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59A LYS* 3.8 23.6 - - - +
60A LYS* 4.6 5.3 + - - +
94A ALA* 1.3 74.4 - - - +
96A TYR* 1.3 65.2 + - - +
97A GLU* 5.3 2.6 - - + +
110A SER* 3.8 25.6 - - - +
111A THR 3.3 8.7 - - - +
112A ARG* 3.5 55.4 - - + +
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Residues in contact with TYR 96 (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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43A PHE* 4.6 8.3 - + + -
57A TRP* 4.9 2.7 - - + -
58A ASN 3.4 13.7 - - - +
59A LYS* 3.9 26.9 + - + +
64A VAL* 4.2 11.4 - - + -
69A PHE* 3.4 37.8 - + - -
82A LEU* 4.3 17.0 - - + -
84A ILE* 4.4 2.5 - - + -
92A ASP* 2.7 31.5 + - - +
94A ALA* 3.6 24.9 - - + +
95A ILE* 1.3 73.9 - - - +
97A GLU* 1.3 66.2 + - - +
110A SER* 3.2 4.7 - - - +
111A THR* 2.8 47.9 + - + +
113A LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 97 (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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56A VAL 3.8 0.3 - - - +
57A TRP* 3.2 12.1 - - - -
58A ASN* 2.9 47.8 + - + +
59A LYS* 6.3 0.2 - - - -
60A LYS 6.0 2.7 - - - +
61A GLY* 4.8 9.0 + - - -
95A ILE* 5.3 2.9 - - + -
96A TYR* 1.3 80.2 - - - +
98A CYS* 1.3 61.0 + - - +
99A VAL* 4.4 13.2 - - + +
108A SER* 4.1 17.4 + - - -
109A VAL 3.3 9.2 - - - +
110A SER* 4.0 17.5 - - - -
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Residues in contact with CYS 98 (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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26A PHE* 3.6 8.5 - - - -
30A PRO* 4.3 2.6 - - + +
45A CYS* 2.0 54.1 - - + -
55A ILE* 3.5 21.8 - - - -
56A VAL 3.7 3.4 - - - -
57A TRP* 3.8 16.8 - - + -
97A GLU* 1.3 71.8 - - - +
99A VAL* 1.3 61.3 + - - +
108A SER* 3.1 4.0 - - - -
109A VAL* 2.9 38.4 + - + +
111A THR* 5.9 0.2 - - - +
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Residues in contact with VAL 99 (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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54A LYS 3.6 1.4 - - - +
55A ILE* 3.2 5.5 - - - -
56A VAL* 2.8 51.8 + - + +
58A ASN* 3.5 28.5 - - - +
97A GLU* 4.4 9.6 - - + +
98A CYS* 1.3 77.8 - - - +
100A ALA* 1.3 59.5 + - - +
101A SER* 5.2 1.9 + - - -
106A GLU* 3.4 41.7 - - + +
107A ILE 3.4 5.6 - - - -
108A SER* 3.8 16.8 - - - -
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Residues in contact with ALA 100 (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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24A PRO* 3.7 13.9 - - + +
26A PHE* 3.9 16.3 - - + -
47A ALA* 3.7 29.8 - - + -
53A PRO* 4.4 2.0 - - + -
54A LYS 3.5 5.2 - - - +
55A ILE* 4.2 7.9 - - + -
98A CYS 4.1 1.0 - - - -
99A VAL* 1.3 72.1 - - - +
101A SER* 1.3 60.8 + - - +
106A GLU* 3.3 3.1 - - - +
107A ILE* 2.9 35.3 + - + -
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Residues in contact with SER 101 (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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24A PRO* 3.8 5.1 - - - +
52A ARG 4.6 0.3 - - - +
53A PRO* 3.2 3.7 - - - +
54A LYS* 3.0 38.6 + - - +
56A VAL* 6.2 0.2 - - - +
99A VAL* 5.2 2.1 + - - -
100A ALA* 1.3 76.3 - - - +
102A ASN* 1.3 63.9 + - - +
105A GLY 3.4 9.0 - - - -
106A GLU* 3.7 24.2 + - - -
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Residues in contact with ASN 102 (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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22A THR 2.9 25.1 + - - -
24A PRO* 3.4 16.4 - - - +
49A GLY* 4.2 1.4 - - - -
50A ASP 3.6 6.7 - - - +
51A PRO* 2.8 40.0 + - + +
52A ARG 4.3 2.0 - - - +
53A PRO* 4.3 4.2 - - + -
101A SER* 1.3 76.9 - - - +
103A ASN* 1.3 64.5 + - - +
104A VAL* 2.9 16.8 + - - +
105A GLY 3.0 27.5 + - - +
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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