Contacts of the strand formed by residues 173 - 179 (chain A) in PDB entry 1MMG
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 GLN 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ALA* 3.3 25.0 - - + +
165A SER* 3.4 22.0 + - - -
166A MET* 3.5 11.9 - - + +
169A ASP* 4.9 0.8 + - - -
171A GLN* 3.0 27.7 + - - +
172A ASN* 1.3 80.8 + - - +
174A SER* 1.3 64.5 + - - +
449A PHE* 3.1 12.1 + - - +
450A ILE* 3.2 18.7 - - + -
451A GLY 3.0 23.0 + - - -
648A THR* 3.6 4.3 - - - -
649A ASN* 2.8 38.9 + - - +
651A HIS* 2.9 21.1 + - + +
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Residues in contact with SER 174 (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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173A GLN* 1.3 77.0 - - - +
175A LEU* 1.4 61.0 + - - +
176A LEU* 3.7 7.6 - - - +
242A PHE* 5.1 2.2 - - - -
451A GLY 3.3 9.9 - - - +
645A LEU* 3.6 25.3 + - - +
648A THR* 2.7 24.2 + - - -
649A ASN 3.0 8.1 + - - -
650A PRO* 3.3 17.3 - - - +
651A HIS* 2.6 37.9 + - - -
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Residues in contact with LEU 175 (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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155A ILE* 5.0 0.2 - - + -
158A ILE* 3.3 28.7 - - + -
159A SER* 4.3 10.1 - - - +
162A ALA* 4.1 15.3 - - + -
174A SER* 1.4 77.7 - - - +
176A LEU* 1.4 57.9 - - - +
177A ILE* 3.8 7.0 - - + -
192A VAL* 4.0 28.5 - - + -
450A ILE* 3.7 28.5 - - + -
451A GLY 2.8 11.7 + - - +
452A VAL* 3.4 18.8 - - + +
453A LEU* 2.9 31.7 + - - +
651A HIS* 3.2 14.4 - - + +
653A VAL* 4.9 5.2 - - + -
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Residues in contact with LEU 176 (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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174A SER* 3.7 26.0 - - - +
175A LEU* 1.4 73.7 - - - +
177A ILE* 1.4 60.0 + - - +
178A THR* 3.9 5.3 + - + -
453A LEU* 4.0 19.1 - - + -
478A LEU* 4.2 30.1 - - + -
481A PHE* 4.2 12.6 - - + -
645A LEU* 4.4 7.6 - - + -
650A PRO* 4.0 12.3 - - + -
651A HIS 2.7 18.9 + - - +
652A PHE* 3.6 26.7 - - + -
653A VAL 2.7 33.3 + - - +
654A ARG* 4.1 6.3 + - - +
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Residues in contact with ILE 177 (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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155A ILE* 4.6 5.8 - - + -
175A LEU* 4.4 5.4 - - + -
176A LEU* 1.4 74.5 - - - +
178A THR* 1.3 62.8 + - - +
185A LYS* 3.7 21.9 - - - +
188A ASN* 4.3 4.3 - - + -
189A THR* 3.4 32.1 - - - +
192A VAL* 4.3 13.9 - - + -
452A VAL* 3.6 19.5 - - + -
453A LEU 2.9 21.6 + - - +
454A ASP* 3.6 2.1 - - - -
455A ILE 3.5 16.6 + - - +
653A VAL* 3.3 24.7 - - + -
655A CYS* 3.7 28.7 - - - -
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Residues in contact with THR 178 (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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176A LEU* 4.7 5.8 - - + -
177A ILE* 1.3 84.7 - - - +
179A GLY* 1.3 59.6 + - - +
185A LYS* 3.4 6.7 - - - -
453A LEU* 4.9 3.8 - - + -
455A ILE* 3.5 29.4 - - + +
457A GLY* 4.2 10.3 - - - -
475A ASN* 4.5 9.4 - - - +
478A LEU* 4.6 11.0 - - + -
653A VAL 3.1 5.1 + - - +
654A ARG* 3.5 30.6 + - - +
655A CYS* 3.0 27.9 + - - +
679A ASN* 5.8 1.2 - - - +
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Residues in contact with GLY 179 (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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178A THR* 1.3 79.3 - - - +
180A GLU* 1.3 62.2 - - - -
183A ALA* 4.3 0.2 - - - -
185A LYS* 2.9 19.7 + - - +
456A SER* 3.6 1.7 - - - -
457A GLY* 3.2 26.1 + - - +
655A CYS 3.5 12.8 - - - -
679A ASN* 6.1 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