Contacts of the strand formed by residues 139 - 145 (chain G) in PDB entry 1YKN
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 LEU 139 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ILE 3.6 0.5 - - - +
129G SER* 3.4 5.9 - - - -
130G LEU* 2.9 42.3 + - + +
135G ILE* 4.2 27.6 - - + -
137G ILE* 4.2 11.2 - - + +
138G HIS* 1.3 75.6 - - - +
140G HIS* 1.3 60.2 + - - +
141G THR* 5.6 0.7 - - - +
189G ILE* 4.4 12.8 - - + -
197G PHE* 3.7 41.7 - - + -
319H ALA* 5.9 2.5 - - + -
330H ARG 5.0 0.9 - - - +
332H PRO* 3.8 29.2 - - + -
336H LEU* 4.5 13.0 - - + -
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Residues in contact with HIS 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ILE 3.2 6.7 + - - +
129G SER* 3.5 14.7 + - - -
138G HIS* 3.5 37.0 + + - -
139G LEU* 1.3 72.0 - - - +
141G THR* 1.3 61.7 + - - +
197G PHE* 3.3 9.6 - - - +
198G PHE* 3.1 43.9 + - + +
199G ASP* 5.1 1.1 - - - -
200G PHE* 3.4 46.9 + + + -
311H ARG* 4.0 14.8 + - - -
313H ARG* 4.2 15.8 + - - -
470H ILE* 4.3 14.4 - - + +
471H ALA* 5.5 0.2 - - - -
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Residues in contact with THR 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G ASN* 3.9 1.2 - - - +
128G ILE* 2.8 57.7 + - + +
130G LEU* 6.3 1.3 - - + -
139G LEU 5.6 0.7 - - - +
140G HIS* 1.3 77.7 - - - +
142G ARG* 1.3 77.1 + - - +
170G LEU* 3.3 13.5 - - - +
185G PHE* 4.5 9.8 - - + -
187G ILE* 4.5 8.7 - - + -
195G THR* 3.8 3.0 - - + +
196G VAL 2.9 22.5 + - - -
197G PHE* 3.9 10.5 - - + -
198G PHE* 3.9 8.8 - - - -
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Residues in contact with ARG 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G MET* 3.5 31.7 - - - +
125G HIS* 3.5 33.5 + - + -
126G ILE 3.4 8.3 - - - +
127G ASN* 3.5 18.2 + - - +
128G ILE 4.6 0.2 - - - +
141G THR* 1.3 93.3 + - - +
143G LEU* 1.3 59.0 + - - +
144G TYR* 3.2 41.0 + - + -
157G VAL* 3.6 20.6 - - - +
170G LEU* 3.6 19.6 - - + +
185G PHE* 3.8 6.2 - - - -
198G PHE* 3.8 23.1 - - + -
339H ILE* 4.5 3.4 - - - +
342H SER* 3.9 1.0 + - - -
344H SER* 3.7 4.6 - - - -
345H GLU* 2.8 28.3 + - - -
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Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LEU* 4.2 21.5 - - + -
104G TRP* 4.6 7.0 - - + -
125G HIS* 3.3 6.4 - - - +
126G ILE* 2.9 40.8 + - + +
128G ILE* 3.9 20.1 - - + +
142G ARG* 1.3 73.3 - - - +
144G TYR* 1.3 70.1 + - - +
145G PHE* 3.8 29.7 - - + -
170G LEU 3.7 3.8 - - - -
172G ALA* 4.0 6.7 - - + -
185G PHE* 3.5 44.2 - - + -
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Residues in contact with TYR 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ALA* 3.5 29.6 - - + -
124G PRO 3.4 15.9 - - - -
125G HIS* 4.0 4.9 - - + -
142G ARG* 3.2 40.9 + - + -
143G LEU* 1.3 77.9 - - - +
145G PHE* 1.3 65.6 + - - +
152G ASN* 3.6 20.0 - - - +
155G CYS* 3.0 25.3 - - - -
157G VAL* 3.7 7.9 - - + +
158G LEU* 3.3 35.3 + - + -
170G LEU* 2.8 25.5 + - + +
171G ILE* 4.3 12.6 - - + -
172G ALA* 2.9 29.3 + - - +
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Residues in contact with PHE 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ILE* 4.1 10.1 - - + -
51G LEU* 4.5 3.4 - - + -
110G LYS* 3.8 15.7 - - + -
111G PRO* 3.8 37.7 - - + -
124G PRO* 3.7 22.6 + - + -
126G ILE* 4.1 10.3 - - + -
143G LEU* 3.8 29.8 - - + -
144G TYR* 1.3 81.3 - - - +
146G ASP* 1.3 62.2 + - - +
147G ASP* 3.5 16.8 - - - +
148G GLU* 3.3 13.2 + - + +
152G ASN* 3.0 22.6 + - - +
171G ILE* 4.0 3.8 - - - -
172G ALA 4.2 1.6 - - - -
183G TYR* 3.7 42.0 - + + -
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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