Contacts of the strand formed by residues 197 - 204 (chain T) in PDB entry 6MZL
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 PHE 197 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.5 49.8 - + + -
38A LEU* 5.3 2.9 - - + -
47A ASN 4.9 0.9 - - - -
48A GLY* 4.7 18.6 - - - -
82A THR* 5.7 2.7 - - + -
192T TYR* 4.8 0.9 - - - -
193T ASN* 2.6 36.8 + - + +
194T PRO* 3.6 2.5 - - - +
195T LYS 4.0 0.2 - - - -
196T ARG* 1.3 79.7 - - + +
198T ALA* 1.3 57.6 + - - +
199T ALA* 3.1 51.2 + - + +
201T ILE* 3.6 17.5 - - + -
212T LEU* 3.6 40.2 - - + -
214T PHE* 5.4 4.5 - + - -
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Residues in contact with ALA 198 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.2 17.5 - - + -
180T LEU* 3.3 21.2 - - - +
192T TYR* 4.2 4.9 + - - -
194T PRO* 4.5 14.1 + - + +
196T ARG 4.4 0.2 - - - -
197T PHE* 1.3 73.7 - - - +
199T ALA* 1.3 57.3 + - - +
214T PHE* 5.1 5.6 - - + -
215T SER* 5.0 1.7 + - - -
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Residues in contact with ALA 199 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180T LEU* 4.4 0.4 - - - -
191T GLU 3.8 1.6 - - - +
192T TYR* 4.1 7.5 - - - -
197T PHE* 3.1 27.5 + - + +
198T ALA* 1.3 79.4 - - - +
200T VAL* 1.3 65.2 + - - +
201T ILE* 3.4 18.2 - - - +
212T LEU* 4.5 2.0 - - + -
213T ILE 3.3 21.3 - - - +
214T PHE* 3.6 26.2 - - + -
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Residues in contact with VAL 200 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180T LEU* 3.7 44.4 - - + +
183T ILE* 4.3 10.8 - - + -
184T ALA* 4.9 1.8 - - + +
190T ALA* 4.3 9.4 - - + -
191T GLU 3.4 8.3 - - - +
192T TYR* 3.8 14.4 - - + -
199T ALA* 1.3 70.8 - - - +
201T ILE* 1.3 67.2 + - - +
202T MET* 3.9 26.6 + - + -
211T ALA 3.4 1.6 - - - +
212T LEU* 3.3 6.9 - - - -
213T ILE* 2.9 45.2 + - + +
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Residues in contact with ILE 201 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.3 42.8 - - + +
48A GLY* 5.4 0.2 - - - -
49A ALA 5.7 1.6 - - - +
189T ASN 4.0 0.5 - - - +
190T ALA* 3.5 2.9 - - - -
191T GLU* 2.7 79.2 + - + +
192T TYR* 4.6 2.5 - - - +
193T ASN* 5.3 2.7 - - + +
197T PHE* 3.6 19.1 - - + -
199T ALA 3.4 13.5 - - - +
200T VAL* 1.3 70.8 - - - +
202T MET* 1.3 60.8 + - - +
203T ARG* 4.7 5.0 + - - +
210T THR* 4.4 10.3 - - + -
211T ALA 3.6 3.6 - - - -
212T LEU* 3.7 10.5 - - + -
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Residues in contact with MET 202 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR* 5.7 1.6 - - - -
183T ILE* 3.9 22.9 - - + -
187T ALA* 4.4 10.8 - - + -
188T ARG 4.9 3.1 - - - +
189T ASN 3.7 14.1 - - - +
190T ALA* 4.4 4.0 - - + -
200T VAL* 3.9 8.0 + - + -
201T ILE* 1.3 75.6 - - - +
203T ARG* 1.3 69.3 + - - +
204T ILE* 5.2 2.2 - - + -
210T THR* 3.3 5.5 - - - +
211T ALA 2.9 35.2 + - - +
213T ILE* 3.8 26.0 - - + -
237T TYR* 3.2 31.4 + - + -
240T VAL* 3.7 31.2 - - + -
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Residues in contact with ARG 203 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.0 35.8 + - - +
53A GLU* 3.5 19.5 + - - +
111A SER* 4.3 8.8 - - - -
188T ARG 5.5 0.2 - - - +
189T ASN* 3.6 34.0 + - + +
191T GLU* 2.7 44.1 + - - +
201T ILE* 4.8 4.4 + - - -
202T MET* 1.3 82.6 - - - +
204T ILE* 1.3 68.9 + - - +
209T THR 3.6 4.3 - - - +
210T THR* 3.9 14.6 - - + +
237T TYR* 3.2 4.5 - - - -
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Residues in contact with ILE 204 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR 4.0 8.3 - - - +
111A SER* 3.8 30.3 - - - +
202T MET* 5.2 2.2 - - + -
203T ARG* 1.3 80.3 - - - +
205T ARG* 1.3 61.5 + - - +
206T GLU 3.4 22.2 - - - +
207T PRO* 3.2 25.3 - - + +
208T ARG* 3.5 3.1 - - - +
209T THR* 2.9 42.5 + - - +
233T ALA* 4.6 3.6 - - + -
236T LYS* 4.0 21.8 - - + -
237T TYR* 2.8 35.4 + - + +
240T VAL* 5.1 5.8 - - + -
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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