Contacts of the strand formed by residues 85 - 94 (chain A) in PDB entry 2YRZ
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 SER 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.3 12.1 - - - +
57A LEU* 2.8 59.1 + - - +
58A ASN* 4.4 7.2 + - - +
84A HIS* 1.3 73.5 - - - +
86A TYR* 1.3 62.1 + - - +
105A VAL* 3.8 3.4 - - - -
106A ILE 3.2 11.7 - - - -
107A THR* 4.4 11.6 - - - +
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Residues in contact with TYR 86 (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 TYR* 4.0 10.8 - + - -
55A GLN* 3.2 13.5 - - - +
56A LEU* 3.1 57.9 - - + +
57A LEU 3.9 0.2 - - - +
61A GLU 5.1 2.5 - - - -
80A LEU* 4.1 24.5 - - + -
81A LEU* 3.4 45.7 + - - +
84A HIS* 3.5 20.0 - - + -
85A SER* 1.3 72.6 - - - +
87A VAL* 1.3 59.7 + - - +
88A PHE* 3.2 30.4 - + + -
105A VAL* 3.2 21.2 - - - -
106A ILE* 3.2 15.1 + - + -
108A ILE* 5.0 4.3 - - + -
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Residues in contact with VAL 87 (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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53A GLU 3.2 12.1 - - - +
54A TYR* 3.3 7.6 - - - -
55A GLN* 2.9 44.8 + - + +
57A LEU* 3.6 28.6 - - + +
86A TYR* 1.3 67.5 - - - +
88A PHE* 1.3 60.3 + - - +
89A ARG* 3.5 31.3 + - + +
103A GLU* 3.6 34.8 - - + +
104A GLY 4.9 0.7 - - - +
105A VAL* 4.1 4.5 - - + +
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Residues in contact with PHE 88 (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 LEU* 2.9 29.8 - - + +
26A PHE* 3.6 24.0 - + + -
34A LEU* 4.3 11.4 - - + -
36A VAL* 3.7 15.5 - - + -
52A VAL* 4.1 13.9 - - + -
53A GLU 3.5 2.0 - - - -
54A TYR* 3.2 29.6 - + + -
77A VAL* 3.3 40.4 - - + -
80A LEU* 4.4 3.6 - - + -
86A TYR* 3.2 41.3 + - + -
87A VAL* 1.3 69.2 - - - +
89A ARG* 1.3 61.1 + - - +
90A VAL* 3.8 0.7 - - - -
104A GLY 2.8 27.2 + - - +
106A ILE* 3.6 17.3 - - + -
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Residues in contact with ARG 89 (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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51A SER 3.6 2.4 - - - +
53A GLU* 2.8 43.1 + - + +
55A GLN* 4.0 18.8 + - - -
62A LEU* 6.0 1.6 - - - +
87A VAL* 3.7 39.1 + - + +
88A PHE* 1.3 70.1 - - - +
90A VAL* 1.3 63.4 + - - +
91A ARG* 3.8 0.5 + - - +
101A GLU* 3.3 35.5 + - - +
102A ARG 3.2 6.5 - - - +
103A GLU* 3.9 26.0 + - + +
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Residues in contact with VAL 90 (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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21A PRO* 3.7 7.8 - - + +
24A LEU* 3.7 23.3 - - + -
36A VAL* 3.5 32.3 - - + -
38A TRP* 3.4 44.2 - - + -
50A TYR* 4.5 0.2 - - + -
51A SER 3.4 7.6 - - - +
52A VAL* 4.1 12.8 - - + -
88A PHE 4.8 0.4 - - - +
89A ARG* 1.3 72.5 - - - +
91A ARG* 1.3 69.6 + - - +
101A GLU* 2.9 23.1 - - - -
102A ARG 3.0 12.2 + - - -
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Residues in contact with ARG 91 (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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21A PRO* 4.9 1.8 - - - -
50A TYR* 3.2 11.3 - - - -
51A SER* 2.7 41.7 + - - +
53A GLU* 3.5 24.9 + - - +
64A ARG* 3.9 21.2 - - - +
89A ARG 4.9 0.7 - - - +
90A VAL* 1.3 76.5 - - - +
92A ALA* 1.3 72.3 + - - +
98A TRP* 3.2 38.6 - - + +
99A GLY 4.0 16.2 - - - +
100A ARG 3.4 16.8 - - - +
101A GLU* 3.7 29.2 + - + +
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Residues in contact with ALA 92 (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 PRO* 3.4 25.4 - - + +
19A ASP 5.5 0.2 - - - +
21A PRO* 5.3 2.8 - - + +
41A PRO* 4.1 10.8 - - + -
47A LEU* 4.2 3.1 - - + -
49A GLY 4.2 0.4 - - - -
50A TYR* 3.4 30.1 - - + -
91A ARG* 1.3 77.0 - - - +
93A GLN* 1.3 61.3 + - - +
98A TRP* 3.2 13.4 - - - -
99A GLY 3.3 20.1 + - - -
100A ARG 4.0 5.8 + - - +
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Residues in contact with GLN 93 (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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47A LEU* 3.4 8.9 - - - +
48A GLN* 2.9 47.3 + - - +
49A GLY* 3.5 16.3 + - - +
92A ALA* 1.3 73.8 - - - +
94A SER* 1.3 70.8 + - - +
97A GLY* 3.8 10.3 - - - +
98A TRP* 3.2 57.4 - - + +
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Residues in contact with SER 94 (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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16A GLY 3.2 22.9 + - - -
18A PRO* 3.6 15.0 - - - +
43A CYS* 5.0 0.2 - - - -
45A ARG* 4.1 9.3 - - - +
46A PRO 4.0 12.1 - - - -
47A LEU* 4.0 12.6 - - - +
48A GLN* 4.2 7.0 - - - +
93A GLN* 1.3 79.7 - - - +
95A GLN* 1.3 57.2 + - - +
96A GLU* 2.5 25.3 + - - +
97A GLY* 2.9 17.5 + - - -
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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