Contacts of the helix formed by residues 145 - 152 (chain L) in PDB entry 3IS7
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 GLY 145 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLU* 4.1 15.3 + - - -
141L ILE 3.1 15.3 + - - -
142L GLN 4.3 1.3 + - - -
143L LYS 3.5 1.6 - - - -
144L VAL* 1.3 83.2 - - - +
146L LEU* 1.3 68.3 + - - -
147L GLU 3.3 2.4 + - - -
148L ASN 3.4 1.0 + - - -
149L TYR* 2.9 20.8 + - - +
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Residues in contact with LEU 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L THR* 5.0 6.7 - - - -
84L GLN* 5.0 13.2 - - + +
141L ILE* 3.8 35.9 + - + +
145L GLY* 1.3 71.9 - - - -
147L GLU* 1.3 68.3 + - + +
149L TYR* 3.3 4.6 + - + +
150L LEU* 2.9 57.0 + - + +
143M LYS 5.8 0.7 - - - +
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Residues in contact with GLU 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L GLY 3.3 0.8 - - - -
146L LEU* 1.3 81.6 - - + +
148L ASN* 1.3 56.5 + - - +
150L LEU* 3.5 0.7 + - - +
151L GLN* 3.0 27.2 + - - +
142M GLN 4.7 4.0 - - - +
143M LYS 3.9 18.4 - - - +
144M VAL* 3.3 27.8 - - - +
145M GLY* 3.9 15.9 + - - -
148M ASN* 3.6 10.0 + - - +
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Residues in contact with ASN 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU* 3.7 18.0 + - - +
148A ASN* 3.0 21.1 + - - +
151A GLN* 3.0 28.7 + - - +
160A K 3.0 11.8 - - - -
144L VAL* 3.2 30.9 + - + +
145L GLY* 3.4 1.4 + - - -
146L LEU 3.3 0.4 - - - -
147L GLU* 1.3 74.4 - - - +
149L TYR* 1.3 60.6 + - - +
151L GLN* 3.1 0.7 + - - -
152L SER* 2.8 29.0 + - - -
148M ASN* 2.9 23.0 + - - +
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Residues in contact with TYR 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A MET* 4.4 4.5 - - + -
40L LEU* 3.9 26.3 - - + +
83L THR* 4.2 6.7 - - + -
87L LEU* 4.2 1.8 - - + +
137L GLN* 2.8 58.3 + - + +
140L LEU* 4.0 19.7 - - + -
141L ILE* 3.5 34.5 - - + -
144L VAL* 3.6 9.7 - - + +
145L GLY 2.9 18.5 + - - +
146L LEU* 3.6 3.8 - - + +
148L ASN* 1.3 77.7 - - - +
150L LEU* 1.3 72.6 + - + +
152L SER* 3.4 3.7 + - - -
153L HIS* 2.8 55.7 + + - -
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Residues in contact with LEU 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L LEU* 3.3 35.2 - - + +
40L LEU* 4.6 2.5 - - + -
83L THR* 3.5 39.7 - - + +
146L LEU* 2.9 37.9 + - + +
147L GLU 3.9 0.9 - - - +
149L TYR* 1.3 79.8 - - + +
151L GLN* 1.3 62.0 + - - +
153L HIS* 3.0 17.3 + - - +
154L MET* 3.3 2.1 + - - +
143M LYS* 3.7 37.9 - - + +
144M VAL* 3.7 14.6 - - + -
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Residues in contact with GLN 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 2.8 23.6 + - - +
160A K 2.9 15.8 - - - -
147L GLU 3.0 18.1 + - - +
148L ASN 3.4 2.7 - - - +
150L LEU* 1.3 75.7 - - - +
152L SER* 1.3 59.6 + - - +
153L HIS 3.0 5.4 + - - -
154L MET* 3.2 21.5 + - - +
155L HIS* 4.8 1.2 + - - -
144M VAL* 3.8 12.7 - - + +
148M ASN* 2.9 29.2 + - + +
151M GLN* 2.8 27.3 + - - +
152M SER* 2.8 30.4 + - - +
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Residues in contact with SER 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 2.9 36.3 + - - +
154A MET* 3.9 23.6 - - - -
155A HIS* 3.3 27.1 - - - -
39L ARG* 3.6 8.1 + - - -
148L ASN 2.8 10.7 + - - -
149L TYR 3.7 6.3 - - - -
150L LEU 3.3 0.2 - - - -
151L GLN* 1.3 75.1 - - - +
153L HIS* 1.3 58.8 + - - +
154L MET 3.5 1.1 + - - -
155L HIS 4.6 1.8 - - - +
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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