Contacts of the strand formed by residues 107 - 115 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C ASP* 2.8 32.3 + - + +
26C LEU 3.4 7.9 - - - +
27C ARG* 3.6 48.8 - - + +
61C ARG* 3.6 40.4 + - - +
64C THR* 4.9 0.7 + - - -
68C PHE* 3.9 15.6 - - - -
105C GLY 3.4 1.5 + - - +
106C ASP* 1.3 71.2 - - - +
108C ILE* 1.3 58.9 + - - +
109C CYS 3.9 0.4 - - - -
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU 2.9 8.3 + - - +
28C ALA 4.4 7.0 - - - +
42C VAL* 4.6 5.8 - - + -
44C LEU* 3.6 30.5 - - + -
61C ARG* 3.9 2.7 + - - -
64C THR* 3.0 34.2 + - + +
68C PHE* 3.5 35.0 - - + -
70C VAL* 4.5 2.5 - - + -
92C PHE* 4.0 26.8 - - + -
102C ILE* 3.6 36.8 - - + -
106C ASP 3.3 4.9 + - - +
107C ARG* 1.3 74.2 - - - +
109C CYS* 1.3 68.6 + - + +
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Residues in contact with CYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASP* 3.6 2.9 - - - -
26C LEU* 2.9 33.0 + - - +
44C LEU* 3.6 35.4 - - - -
58C VAL* 3.6 17.3 - - + -
59C VAL 3.2 15.5 - - - +
61C ARG* 3.7 13.8 - - - +
92C PHE* 3.5 24.7 - - + -
108C ILE* 1.3 78.5 - - - +
110C GLN* 1.3 63.7 + - - +
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Residues in contact with GLN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 4.0 20.8 - - - +
23C TRP* 3.5 39.7 - - + +
24C ILE 3.1 13.5 - - - +
25C ASP* 3.8 12.5 - - - +
26C LEU* 4.4 1.6 - - - +
58C VAL* 3.4 6.1 - - - +
59C VAL* 2.9 44.2 + - + +
60C PRO 3.8 9.0 - - - +
61C ARG* 3.8 17.9 - - - +
62C SER 4.6 2.6 + - - -
109C CYS* 1.3 78.2 - - - +
111C PHE* 1.3 60.7 + - - +
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Residues in contact with PHE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A MET* 4.1 1.2 - - - +
122A LEU* 5.4 2.0 - - + -
3C ILE* 4.2 21.1 - - + -
15C ILE* 4.2 3.8 - - + -
23C TRP* 3.4 9.5 - - - -
24C ILE* 2.8 79.8 + - + +
26C LEU* 3.7 20.6 - - + -
48C MET* 3.9 28.0 - - + -
50C LEU* 4.9 0.2 - - + -
56C ALA* 4.0 2.5 - - + -
57C HIS 3.1 13.2 - - - +
58C VAL* 4.1 6.1 - - + -
90C TRP* 3.8 30.1 - + + -
110C GLN* 1.3 74.3 - - - +
112C ARG* 1.3 74.2 + - - +
113C ILE* 4.2 9.6 - - + -
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.0 27.8 + - - +
57A HIS* 5.1 0.4 - - - -
114A MET* 4.1 13.1 - - - -
115A LYS 2.8 26.2 + - - -
116A LYS 4.2 0.2 + - - -
117A MET* 3.3 44.4 - - + +
118A PRO* 4.8 2.0 - - - +
23C TRP* 3.4 46.2 - - + +
56C ALA* 3.3 5.5 - - - +
57C HIS* 2.9 34.0 + - + -
111C PHE* 1.3 80.5 - - - +
113C ILE* 1.3 86.0 + - - +
114C MET* 3.9 26.6 - - + +
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Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A MET* 3.4 24.8 - - + +
118A PRO* 4.7 6.3 - - + +
120A VAL* 4.9 13.5 - - + -
1C MET* 3.8 23.6 - - - -
3C ILE* 3.9 23.6 - - + -
50C LEU* 4.1 15.5 - - + -
51C PRO* 3.9 12.1 - - + -
54C TYR* 3.7 25.6 - - + -
55C GLU 3.1 12.1 - - - +
56C ALA* 4.7 0.9 - - - -
111C PHE* 4.2 7.4 - - + -
112C ARG* 1.3 103.0 + - - +
114C MET* 1.3 62.3 + - - +
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Residues in contact with MET 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A HIS* 5.1 2.9 - - + -
114A MET* 3.5 31.6 - - + +
118A PRO* 6.3 0.2 - - - -
112B ARG* 4.1 6.7 - - - +
114B MET* 3.7 29.8 - - + +
54C TYR* 3.4 7.5 - - - -
55C GLU* 2.9 31.2 + - + +
57C HIS* 3.5 37.7 - - + +
112C ARG* 3.9 24.2 - - - +
113C ILE* 1.3 73.5 - - - +
115C LYS* 1.3 78.0 + - + +
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 2.9 23.4 + - - -
52C GLU 5.4 0.2 - - - -
53C GLY* 2.9 32.5 + - - +
54C TYR* 3.5 34.3 - - + +
114C MET* 1.3 78.9 - - + +
116C LYS* 1.3 87.4 + - - +
117C MET 5.1 2.4 + - - -
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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