Contacts of the strand formed by residues 93 - 102 (chain B) in PDB entry 1Y7M
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 GLY 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLU* 5.1 11.7 - - - -
92B THR* 1.3 74.9 - - - +
94B GLU* 1.3 65.5 + - - -
95B PHE* 3.5 10.8 - - - -
161B THR* 3.6 2.8 - - - -
162B ILE 2.9 34.5 + - - -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 2.6 26.3 + - - -
94A GLU* 5.4 12.7 - - - +
159A ARG* 4.2 10.1 + - - +
93B GLY* 1.3 73.2 - - - -
95B PHE* 1.3 69.2 + - - +
96B TYR* 4.8 5.6 - - - +
116B SER* 4.5 0.9 + - - -
159B ARG* 3.3 30.2 + - - +
160B VAL 3.9 0.2 - - - -
161B THR* 2.6 34.9 + - - +
205B SO4 3.8 24.6 + - - +
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PRO* 3.8 29.8 - - + -
92B THR 3.8 20.9 - - - -
93B GLY 3.5 23.1 - - - -
94B GLU* 1.3 77.6 - - - +
96B TYR* 1.3 77.6 + - - +
115B LEU* 4.2 22.0 - - + -
116B SER* 3.2 30.7 - - - +
117B ALA* 3.8 22.9 - - + -
159B ARG* 3.6 2.4 - - - +
160B VAL* 2.9 33.6 + - + +
162B ILE* 3.8 17.7 - - + -
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.0 34.5 - - + +
3B THR 5.2 2.0 + - - -
4B TYR* 6.4 0.7 - + - -
19B PHE* 4.4 8.7 - + - -
48B LEU* 5.6 0.2 - - + -
51B PRO* 3.7 24.2 - - + +
94B GLU* 4.8 3.6 - - + -
95B PHE* 1.3 85.5 - - - +
97B ILE* 1.3 67.1 + - - +
98B ILE* 3.4 7.7 + - + +
115B LEU* 3.3 9.5 - - - -
116B SER* 3.0 41.1 + - - +
157B GLY* 3.8 21.8 - - - +
158B THR 3.3 7.9 - - - +
159B ARG* 3.3 27.2 + - + -
160B VAL* 4.5 0.4 - - - +
205B SO4 2.2 38.9 + - - -
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.0 1.4 - - - +
58B ILE* 4.6 7.0 - - + -
96B TYR* 1.3 72.1 - - - +
98B ILE* 1.3 61.5 + - - +
99B ASN 4.1 7.4 - - - +
100B ARG* 3.8 13.7 - - - +
113B LEU* 3.8 26.7 - - + -
114B SER 3.4 7.9 - - - +
115B LEU* 4.1 4.3 - - + -
122B ILE* 3.8 21.3 - - + -
154B VAL* 4.9 2.7 - - + -
155B PRO 4.2 7.2 - - - +
156B ASN* 3.8 18.8 - - - +
157B GLY* 2.7 30.5 + - - -
158B THR* 3.0 25.9 + - - +
160B VAL* 3.8 20.9 - - + -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP 4.2 4.0 - - - +
19B PHE* 3.3 54.5 - - + +
20B ARG* 3.8 15.9 - - + +
47B GLY 5.3 0.3 - - - +
48B LEU* 3.6 27.4 - - + +
96B TYR* 3.7 12.8 - - + +
97B ILE* 1.3 73.9 - - - +
99B ASN* 1.3 69.1 + - + +
114B SER* 2.8 15.0 + - - +
115B LEU 3.8 6.1 - - - +
116B SER* 3.7 26.0 - - - +
156B ASN* 3.5 17.3 + - - +
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 3.4 35.4 + - - +
97B ILE* 3.7 4.1 - - - +
98B ILE* 1.3 82.8 - - + +
100B ARG* 1.3 70.6 + - - +
101B GLN* 4.3 9.1 - - - +
113B LEU* 3.5 2.4 - - - -
114B SER* 2.5 48.3 + - - +
156B ASN* 3.6 15.0 + - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.8 11.9 - - - +
99B ASN* 1.3 82.2 + - - +
101B GLN* 1.3 69.8 + - - +
102B ARG 5.1 0.2 - - - +
111B TYR* 3.5 30.1 + - + +
112B TRP* 3.1 14.8 - - - +
113B LEU* 4.1 10.2 - - + +
151B ALA* 3.3 35.5 + - - +
154B VAL* 3.0 22.4 + - - +
155B PRO* 3.4 2.9 - - - -
156B ASN* 2.8 47.3 + - - +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASN* 4.3 9.0 - - - +
100B ARG* 1.3 80.5 - - - +
102B ARG* 1.3 66.2 + - - +
104B PRO* 3.4 11.3 - - + +
111B TYR* 3.3 4.1 - - - -
112B TRP* 2.9 64.3 + - + +
114B SER* 4.5 0.7 + - - -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ARG* 5.1 0.2 - - - +
101B GLN* 1.3 72.2 - - - +
103B ASN* 1.3 89.6 + - + +
104B PRO* 3.2 1.9 - - - +
110B ALA 4.4 1.1 - - - +
111B TYR* 3.4 38.9 - - + +
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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