Contacts of the strand formed by residues 122 - 129 (chain S) in PDB entry 5IY8
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 THR 122 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B GLU* 3.1 22.4 + - + +
547B GLU* 5.6 2.5 - - - -
119S THR* 2.4 34.3 + - - +
121S ASN* 1.3 90.1 - - + +
123S SER* 1.3 62.0 + - - +
124S TYR* 4.8 0.9 - - - -
22T LYS* 3.1 40.3 - - + +
23T VAL 3.2 11.0 - - - -
24T PRO* 3.9 20.0 - - + -
25T LYS* 3.8 4.2 - - - -
115T GLU* 6.0 2.0 - - + -
116T CYS 5.9 1.8 - - - +
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Residues in contact with SER 123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119S THR* 4.1 4.8 + - - -
122S THR* 1.3 77.6 + - - +
124S TYR* 1.3 65.4 + - - +
125S TYR* 3.5 28.9 + - - -
23T VAL* 2.5 37.7 + - - +
25T LYS* 3.4 22.7 - - - +
28T SER* 4.4 4.2 + - - -
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Residues in contact with TYR 124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B ASN* 4.9 3.7 - - - +
555B GLU* 2.2 39.7 + - + -
115S LYS* 4.7 13.7 - - - -
119S THR* 4.2 23.4 + - + +
122S THR* 4.8 0.4 - - - -
123S SER* 1.3 71.7 - - - +
125S TYR* 1.3 71.8 + - - +
140S VAL* 3.2 31.8 + - + +
143S TRP* 4.9 19.1 - + + -
20T LEU* 3.7 23.3 - - + -
21T VAL 3.5 3.4 - - - -
22T LYS* 3.4 53.9 + - + +
86T GLN* 6.0 0.4 - - - -
113T ARG* 4.6 7.8 + - - -
114T ALA 5.5 0.7 - - - -
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Residues in contact with TYR 125 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S VAL* 6.1 5.6 - - + -
123S SER* 4.0 16.9 - - - -
124S TYR* 1.3 84.7 - - - +
126S ILE* 1.3 63.4 + - - +
127S PHE* 3.9 17.8 + + + -
137S ALA* 5.0 4.0 - - + -
138S PHE 3.4 17.9 - - - +
139S PRO* 3.5 24.4 - - + +
140S VAL 4.4 0.7 - - - -
19T TRP 3.5 0.7 - - - +
20T LEU* 3.5 5.9 - - - -
21T VAL* 2.9 35.7 + - - +
23T VAL* 3.5 25.4 - - + -
28T SER* 3.4 34.6 + - - -
31T TRP* 4.0 17.5 - + - -
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Residues in contact with ILE 126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S TYR* 5.7 4.5 - - + -
28S ILE* 4.1 7.0 - - + -
125S TYR* 1.3 72.2 - - - +
127S PHE* 1.3 64.4 + - - +
128S THR 4.8 0.2 - - - +
136S GLU 3.4 1.6 - - - +
137S ALA* 3.1 2.3 - - - -
138S PHE* 2.5 62.7 + - + +
140S VAL* 4.3 14.3 - - + +
18T VAL* 3.8 26.9 - - + -
19T TRP 3.2 10.8 - - - +
20T LEU* 4.1 16.8 - - + -
95T VAL* 3.8 34.1 - - + -
110T VAL* 4.0 14.6 - - + -
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Residues in contact with PHE 127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S VAL* 3.6 32.1 - - + -
125S TYR* 4.0 15.3 - + + -
126S ILE* 1.3 79.1 - - - +
128S THR* 1.3 60.0 + - - +
135S PHE* 4.2 30.1 - + + -
136S GLU 3.2 3.8 - - - -
137S ALA* 3.9 21.1 - - + -
18T VAL* 3.5 3.1 - - - -
19T TRP* 2.6 59.5 + - + +
21T VAL* 3.4 36.3 - - + -
23T VAL* 5.4 1.1 - - + -
31T TRP* 4.7 16.2 - + - -
43T LEU* 5.5 4.5 - - + -
56T PHE* 5.8 1.8 - + - -
83T PHE* 5.0 12.3 - + - -
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Residues in contact with THR 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126S ILE* 4.0 0.6 + - - -
127S PHE* 1.3 74.1 - - - +
129S GLN* 1.3 67.0 + - - +
130S CYS* 3.8 7.8 + - - -
135S PHE* 3.6 6.9 - - - -
136S GLU* 2.5 61.5 + - + +
138S PHE* 4.1 23.3 - - + -
16T THR* 5.3 4.9 - - - +
17T GLY 4.4 3.9 + - - -
18T VAL* 3.9 21.6 - - - +
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Residues in contact with GLN 129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S TYR* 4.6 22.0 + - - -
128S THR* 1.3 81.4 + - - +
130S CYS* 1.3 72.7 + - - +
131S PRO* 4.3 3.5 - - - +
133S GLY* 5.6 4.8 - - - -
134S ALA 4.2 4.5 - - - +
135S PHE* 3.7 25.8 - - + -
17T GLY 5.1 3.6 + - - -
19T TRP* 6.2 1.0 - - - -
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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