Contacts of the helix formed by residues 200 - 206 (chain A) in PDB entry 1N1M
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 ASP 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A TRP* 5.7 0.4 - - - -
195A TYR* 4.0 22.2 - - + +
199A THR* 1.3 74.6 - - - +
201A TRP* 1.3 65.4 + - - +
202A VAL* 3.1 10.7 + - - +
203A TYR* 2.7 27.1 + - - +
204A GLU* 3.0 17.1 + - - +
228A PHE* 4.1 6.3 - - + -
230A ASP* 2.6 39.2 - - - +
255A PRO 5.4 1.8 - - - +
257A PRO* 5.1 1.7 - - - +
264A PRO* 3.2 23.6 - - - +
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Residues in contact with TRP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 3.4 46.5 - + - +
195A TYR* 5.3 2.6 + - - -
200A ASP* 1.3 73.3 - - - +
202A VAL* 1.3 72.0 + - + +
204A GLU* 3.4 4.4 + - - +
205A GLU* 3.1 47.9 + - + +
254A VAL* 3.8 14.3 - - + +
255A PRO* 3.7 20.7 + - - +
256A TYR* 3.2 34.8 - + + -
663A ASP* 3.6 23.6 - - + -
709A ASP* 2.6 44.7 + - + -
710A ASN* 3.7 26.0 - - + -
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASP* 3.1 18.7 + - - +
201A TRP* 1.3 87.4 - - + +
203A TYR* 1.3 68.9 + - + +
206A GLU* 2.8 44.1 + - + +
207A VAL* 3.6 1.4 + - - +
255A PRO 5.0 0.4 + - - -
257A PRO* 3.9 26.9 - - + -
264A PRO* 4.3 11.2 - - + -
299A TYR* 6.3 0.4 - - + -
663A ASP* 4.0 17.5 - - + -
665A VAL* 3.5 29.6 - - + -
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A THR* 3.6 18.8 - - + -
200A ASP* 2.7 23.7 + - - +
202A VAL* 1.3 76.7 - - + +
204A GLU* 1.3 61.4 + - - +
207A VAL* 3.0 28.0 + - + +
208A PHE* 2.9 41.6 + + - +
228A PHE* 3.3 41.5 - + + -
264A PRO* 4.0 24.1 + - + -
266A VAL* 3.8 9.4 - - + +
298A HIS 4.1 1.4 + - - -
299A TYR* 3.1 27.7 - + - +
300A LEU* 3.1 42.2 + - + -
665A VAL* 6.1 0.2 - - + -
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 3.4 23.8 - - - +
125A ARG* 3.4 1.2 + - + -
126A HIS* 2.6 41.1 + - + -
127A SER* 2.8 36.5 + - - -
199A THR* 3.1 13.2 + - - +
200A ASP 3.0 8.5 + - - +
201A TRP* 3.5 8.5 - - - +
203A TYR* 1.3 78.2 - - - +
205A GLU* 1.3 60.8 + - + +
209A SER* 3.1 27.7 - - - -
210A ALA 3.2 23.8 + - - +
211A TYR* 3.5 9.1 - - - -
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 6.0 0.6 - - + +
125A ARG* 2.8 56.1 + - - +
126A HIS* 5.3 1.9 + - - -
201A TRP* 3.1 39.1 + - + +
204A GLU* 1.3 83.4 - - + +
206A GLU* 1.3 82.8 + - - +
209A SER* 4.3 9.8 - - - -
358A ARG* 4.7 1.7 + - - -
662A TYR* 4.6 0.9 - - - +
710A ASN* 4.2 6.4 + - - -
954A A3M 3.0 24.7 + - - +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL* 2.8 24.6 + - + +
205A GLU* 1.3 83.4 - - + +
207A VAL* 1.3 59.2 + - - +
209A SER 4.8 0.2 - - - -
357A PHE 4.5 0.3 - - - +
358A ARG* 3.0 20.1 + - - -
662A TYR* 3.1 6.4 + - - -
663A ASP* 2.4 42.5 - - - +
665A VAL* 3.4 23.1 - - + -
666A TYR* 3.4 18.5 - - - +
669A ARG* 4.3 16.0 + - - +
954A A3M 2.8 36.2 + - - +
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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