Contacts of the strand formed by residues 74 - 80 (chain A) in PDB entry 2Y1Z
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 ARG 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ARG 4.7 0.2 - - - -
71A GLU* 2.9 46.7 + - + +
72A LYS 3.5 0.6 - - - -
73A ASP* 1.3 96.7 + - + +
75A PHE* 1.3 64.5 + - - +
76A SER* 6.0 1.6 - - - -
146A ASN* 4.1 29.0 + - + +
147A GLY* 3.9 7.1 - - - +
148A PRO* 3.9 26.0 - - + +
149A ARG* 3.8 9.4 - - - +
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Residues in contact with PHE 75 (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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68A MET* 4.1 24.2 - - + -
69A ARG 3.4 16.2 - - - -
70A LEU* 3.7 27.6 - - + -
74A ARG* 1.3 77.2 - - - +
76A SER* 1.3 65.8 + - - +
77A VAL* 3.7 28.9 - - + -
98A ILE* 4.4 16.2 - - + -
122A TYR* 5.3 0.4 - - + -
123A ARG 4.3 9.6 - - - -
124A ILE* 4.7 4.3 - - + -
125A PRO* 3.6 35.4 - - + -
128A VAL* 4.3 10.3 - - + -
133A ILE* 5.5 2.5 - - + -
145A VAL 5.2 1.1 - - - -
146A ASN* 3.3 4.3 - - - +
147A GLY 3.1 36.2 + - - +
149A ARG* 4.4 0.4 - - + -
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Residues in contact with SER 76 (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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68A MET* 3.7 0.2 - - - -
69A ARG* 2.7 52.2 + - - +
71A GLU* 5.0 6.5 + - - -
74A ARG* 6.0 1.8 - - - -
75A PHE* 1.3 77.5 - - - +
77A VAL* 1.3 64.7 + - - +
78A ASN* 3.5 16.7 + - - -
144A THR* 4.1 11.9 - - - -
145A VAL 3.3 5.2 - - - -
146A ASN* 3.7 16.4 - - - -
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Residues in contact with VAL 77 (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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67A GLU 3.9 6.3 - - - +
68A MET* 4.0 9.0 - - + -
75A PHE* 3.7 25.6 - - + -
76A SER* 1.3 78.7 - - - +
78A ASN* 1.3 68.6 + - - +
79A LEU* 4.9 6.5 - - + +
98A ILE* 4.7 4.0 - - + -
122A TYR* 3.5 55.4 - - + +
143A LEU 3.5 2.3 - - - +
144A THR* 3.2 4.9 - - - -
145A VAL* 2.8 46.6 + - + +
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Residues in contact with ASN 78 (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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67A GLU* 3.1 37.9 + - + +
69A ARG* 2.8 34.6 + - - +
76A SER* 3.5 15.7 + - - -
77A VAL* 1.3 74.1 - - - +
79A LEU* 1.3 64.8 + - - +
142A VAL* 4.3 11.1 - - + +
143A LEU 3.4 1.3 - - - +
144A THR* 2.5 41.2 + - - +
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Residues in contact with LEU 79 (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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67A GLU 5.5 1.3 - - - +
77A VAL* 4.9 6.1 - - + +
78A ASN* 1.3 77.8 - - - +
80A ASP* 1.3 65.2 + - - +
81A VAL* 4.2 6.1 - - + -
100A VAL* 3.6 31.0 - - + -
118A PHE* 4.0 13.9 - - + -
122A TYR* 3.8 17.9 - - + +
142A VAL* 3.3 10.0 - - - +
143A LEU* 2.7 63.4 + - + +
145A VAL* 5.8 2.0 - - + -
114B ILE* 3.8 29.8 - - + -
116B ARG* 5.9 3.1 - - - +
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Residues in contact with ASP 80 (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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79A LEU* 1.3 72.5 - - - +
81A VAL* 1.3 68.7 + - - +
82A LYS* 3.1 24.8 + - - +
140A ASP 5.1 1.6 - - - +
141A GLY 3.7 6.0 - - - +
142A VAL* 4.9 7.0 - - + +
82B LYS* 4.4 14.7 + - - +
83B HIS* 2.7 39.2 + - + +
116B ARG* 3.6 21.1 + - - -
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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