Contacts of the strand formed by residues 107 - 115 (chain A) in PDB entry 2Y1T
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASN* 4.7 10.5 - - - +
25A ASP* 3.1 32.2 + - + +
26A LEU 3.5 7.9 - - - +
27A ARG* 3.4 50.0 - - + +
61A ARG* 3.6 41.8 + - - +
64A THR* 5.0 0.9 + - - -
68A PHE* 3.7 19.9 - - - -
105A GLY 3.5 2.5 + - - +
106A ASP* 1.3 70.6 - - - +
108A ILE* 1.3 58.7 + - - +
109A CYS 3.9 0.4 - - - -
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Residues in contact with ILE 108 (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 LEU 3.0 5.3 + - - +
28A ALA* 4.1 8.1 - - + +
42A VAL* 3.2 34.8 - - + -
44A LEU* 3.3 27.1 - - + -
61A ARG* 4.0 2.4 + - - -
64A THR* 3.2 31.9 + - + +
68A PHE* 4.5 12.1 - - + -
70A VAL* 6.0 0.4 - - + -
92A PHE* 3.9 25.0 - - + -
102A ILE* 4.0 33.2 - - + -
106A ASP 4.2 3.1 - - - +
107A ARG* 1.3 78.9 - - - +
109A CYS* 1.3 67.2 + - - +
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Residues in contact with CYS 109 (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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25A ASP* 3.5 5.0 - - - -
26A LEU* 2.9 35.3 + - - +
44A LEU* 3.8 30.3 - - - -
58A VAL* 3.7 21.8 - - + -
59A VAL 3.2 15.7 - - - +
61A ARG* 3.7 14.8 - - - +
92A PHE* 3.5 24.0 - - + -
107A ARG 3.9 0.4 - - - -
108A ILE* 1.3 77.8 - - - +
110A GLN* 1.3 61.6 + - - +
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Residues in contact with GLN 110 (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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23A TRP* 3.5 41.0 - - + +
24A ILE 3.3 11.0 - - - +
25A ASP* 3.7 13.6 - - - +
26A LEU* 4.6 1.3 - - - +
57A HIS 3.6 0.3 - - - +
58A VAL* 3.3 5.8 - - - +
59A VAL* 2.9 46.1 + - + +
60A PRO 3.8 9.8 + - - +
61A ARG* 4.0 15.6 - - + +
62A SER* 4.9 0.8 + - - -
109A CYS* 1.3 77.3 - - - +
111A PHE* 1.3 61.2 + - - +
78B VAL* 3.7 24.0 - - - +
143B DUD 4.7 13.2 + - - -
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Residues in contact with PHE 111 (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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3A ILE* 4.3 11.2 - - + -
15A ILE* 4.2 4.0 - - + -
18A MET* 4.5 2.5 - - + -
23A TRP* 3.5 8.0 - - - -
24A ILE* 2.9 75.4 + - + +
26A LEU* 3.7 22.7 - - + -
48A MET* 3.8 30.1 - - + -
50A LEU* 5.0 0.4 - - + -
56A ALA* 4.0 2.5 - - + -
57A HIS 3.0 15.3 - - - +
58A VAL* 3.9 14.8 - - + -
90A TRP* 3.9 19.1 - + + -
110A GLN* 1.3 74.7 - - - +
112A ARG* 1.3 70.6 + - - +
113A ILE* 4.1 19.7 - - + -
117B MET* 4.2 1.4 - - - +
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Residues in contact with ARG 112 (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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23A TRP* 3.4 47.7 - - + +
56A ALA* 3.3 4.9 - - - +
57A HIS* 2.9 31.3 + - + -
111A PHE* 1.3 77.5 - - - +
113A ILE* 1.3 84.7 + - - +
114A MET* 3.9 30.5 - - + +
55B GLU* 3.0 20.7 + - - -
57B HIS* 5.0 0.7 - - - -
114B MET* 4.1 10.3 - - - +
115B LYS 2.9 28.7 + - - -
116B LYS 3.9 0.6 + - - -
117B MET* 3.5 45.6 - - + +
118B PRO* 5.0 2.4 - - - +
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Residues in contact with ILE 113 (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 MET* 4.2 9.9 - - + -
3A ILE* 4.1 13.5 - - + -
50A LEU* 3.9 27.8 - - + -
51A PRO* 3.9 22.9 - - + -
54A TYR* 3.6 28.0 - - + -
55A GLU 3.2 11.2 - - - +
56A ALA* 4.3 1.6 - - + -
57A HIS* 6.1 0.2 - - - -
111A PHE* 4.1 7.4 - - + -
112A ARG* 1.3 102.1 + - - +
114A MET* 1.3 61.8 - - - +
117B MET* 3.4 22.3 - - + +
118B PRO* 5.0 4.1 - - + +
120B VAL* 4.7 13.9 - - + -
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Residues in contact with MET 114 (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* 3.2 10.0 - - - -
55A GLU* 2.9 30.2 + - - +
57A HIS* 3.3 38.6 - - + +
112A ARG* 3.9 29.2 - - - +
113A ILE* 1.3 73.2 - - - +
115A LYS* 1.3 73.8 + - + +
57B HIS* 5.0 4.0 - - + -
114B MET* 3.7 24.9 - - + +
112C ARG* 4.1 6.5 - - - +
114C MET* 3.5 35.2 - - + +
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Residues in contact with LYS 115 (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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52A GLU 5.4 0.2 - - - -
53A GLY* 2.8 39.2 + - - -
54A TYR* 3.4 31.2 - - + +
114A MET* 1.3 79.0 - - + +
116A LYS* 1.3 85.7 + - - +
117A MET 5.2 2.0 + - - -
118A PRO* 6.3 0.6 - - + +
112C ARG* 2.8 25.1 + - - -
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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