Contacts of the helix formed by residues 158 - 167 (chain K) in PDB entry 6T9L
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 ASN 158 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K CYS 3.2 16.2 + - - +
155K LEU* 3.6 22.2 - - - +
156K ILE 3.3 2.8 - - - -
157K HIS* 1.3 76.3 - - - +
159K PRO* 1.3 72.1 - - - +
160K TYR* 3.8 13.1 + - - +
161K PHE* 3.1 21.6 + - + +
162K ILE* 2.9 30.1 + - - +
279K PHE* 3.9 26.6 - - - -
357K VAL* 5.1 5.4 - - - +
414K ILE* 4.9 9.3 - - - +
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Residues in contact with PRO 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K HIS 3.4 9.8 - - - +
158K ASN* 1.3 93.4 - - - +
160K TYR* 1.3 70.3 + - + +
162K ILE* 3.9 10.7 - - + +
163K ARG* 3.3 23.6 + - - +
414K ILE* 5.2 9.4 - - + -
466K THR* 5.8 3.6 - - + +
65N ILE* 4.5 5.9 - - + +
68N PRO* 3.8 39.5 - - + +
69N LEU* 4.5 12.3 - - + -
73N ILE* 5.3 8.5 - - + -
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Residues in contact with TYR 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158K ASN* 3.2 12.4 + - - +
159K PRO* 1.3 85.1 - - + +
161K PHE* 1.3 63.6 + - - +
163K ARG* 3.7 10.5 + - - +
164K HIS* 3.2 22.7 + - - +
274K ILE* 4.4 8.1 - - + +
278K VAL* 3.8 22.4 - - + -
279K PHE* 5.8 0.4 - - + -
356K SER* 3.2 23.6 - - - -
357K VAL* 3.6 25.1 - - + -
466K THR* 4.2 9.4 + - - -
467K ILE* 3.3 25.8 - - - +
63N GLN* 3.9 19.2 + - + +
64N LEU* 4.6 0.7 - - - -
65N ILE* 3.4 53.1 + - + -
68N PRO* 5.5 3.2 - - + +
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Residues in contact with PHE 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K LEU* 3.2 45.5 - - + +
156K ILE* 5.2 2.7 - - + -
158K ASN* 3.1 18.6 + - - +
160K TYR* 1.3 76.8 - - - +
162K ILE* 1.3 56.1 + - + +
164K HIS* 3.8 12.3 - - + -
165K SER* 2.6 46.5 + - - -
187K LEU* 4.0 39.5 - - + -
188K ASP* 5.5 2.0 - - - -
191K VAL* 4.0 25.1 - - + -
249K ILE* 5.1 9.2 - - + -
274K ILE* 5.4 13.5 - - + -
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Residues in contact with ILE 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K LEU 5.0 0.9 - - - +
156K ILE 3.2 26.5 - - - +
157K HIS* 4.2 6.1 - - - +
158K ASN 2.9 25.3 + - - +
159K PRO* 3.9 5.8 - - + +
161K PHE* 1.3 79.0 - - + +
163K ARG* 1.3 59.3 + - - +
165K SER* 2.9 6.9 + - - +
166K MET* 2.8 58.3 + - + +
191K VAL* 6.6 0.4 - - + -
195K TYR* 3.4 22.0 - - + +
73N ILE* 3.7 35.0 - - + -
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Residues in contact with ARG 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K PRO 3.3 15.1 + - - +
160K TYR* 3.7 6.6 + - - +
162K ILE* 1.3 81.4 - - - +
164K HIS* 1.3 51.5 + - - +
166K MET* 4.7 3.3 - - - +
167K SER* 2.6 36.6 + - - -
63N GLN* 2.8 48.1 + - - +
64N LEU 4.4 5.7 + - - +
65N ILE* 3.4 38.0 - - + +
86N ALA* 5.4 6.1 - - + +
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Residues in contact with HIS 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K TYR 3.2 18.0 + - - +
161K PHE* 3.4 12.5 + - - +
162K ILE 3.2 0.4 - - - -
163K ARG* 1.3 77.8 - - - +
165K SER* 1.3 61.6 + - - +
167K SER* 2.9 14.5 + - - -
168K GLN 4.2 3.3 + - - -
169K ILE* 4.2 30.9 + - + +
170K HIS* 5.0 14.0 + - + -
249K ILE* 6.1 2.0 - - + -
253K TYR* 6.2 2.0 - - - -
274K ILE* 3.5 50.7 + - + +
63N GLN* 5.3 4.3 - - - +
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Residues in contact with SER 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K PHE* 2.6 39.7 + - - -
162K ILE* 2.9 16.3 + - - -
164K HIS* 1.3 76.0 - - - +
166K MET* 1.3 63.6 + - - +
167K SER 3.2 2.0 - - - -
168K GLN* 3.2 23.9 + - - +
188K ASP* 4.1 22.7 - - - +
191K VAL* 4.3 22.6 - - - +
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Residues in contact with MET 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162K ILE* 2.8 31.4 + - + +
163K ARG* 4.7 2.2 - - - +
165K SER* 1.3 78.1 - - - +
167K SER* 1.3 60.2 + - - +
168K GLN* 3.2 11.3 + - - +
191K VAL* 6.3 2.0 - - + -
195K TYR* 3.6 31.6 - - + -
73N ILE* 3.7 12.6 - - + -
74N GLN 5.1 1.1 - - - +
75N TYR* 3.6 46.7 - - + -
84N PRO* 3.6 30.3 - - + +
85N LEU* 3.7 2.4 - - - -
86N ALA* 3.1 34.4 + - + +
89N ALA* 4.5 1.0 - - - +
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Residues in contact with SER 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K ARG* 2.6 27.1 + - - -
164K HIS* 2.9 17.2 + - - -
166K MET* 1.3 72.7 - - - +
168K GLN* 1.3 69.3 + - - +
169K ILE* 3.3 26.8 + - - +
172K ASN* 4.3 3.6 + - - -
86N ALA* 4.4 7.1 - - - +
88N THR* 5.7 2.9 - - - -
89N ALA* 3.9 20.1 - - - +
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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