Contacts of the strand formed by residues 649 - 656 (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 ASN 649 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A SER* 4.1 10.9 + - - -
169A ASP* 5.2 2.6 + - - -
171A GLN* 3.5 23.1 + - - +
172A ASN 2.8 8.1 + - - -
173A GLN* 2.8 32.0 + - - +
174A SER 3.0 17.8 + - - -
485A HIS* 4.3 8.3 + - - -
648A THR* 1.4 71.3 - - - +
650A PRO* 1.3 71.7 - - - +
651A HIS* 3.4 21.5 + - - -
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Residues in contact with PRO 650 (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* 3.3 20.0 - - - +
176A LEU* 4.0 2.9 - - + -
481A PHE* 3.7 27.1 - - + -
485A HIS* 3.5 42.6 + - + +
648A THR 3.7 8.2 - - - +
649A ASN* 1.3 89.6 - - - +
651A HIS* 1.4 68.2 + - - +
652A PHE* 3.7 22.4 - - + -
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Residues in contact with HIS 651 (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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121A LEU 5.8 0.4 - - - -
158A ILE* 4.1 22.3 + - + +
161A VAL* 4.1 19.8 - - + +
162A ALA* 3.8 28.9 - - + +
165A SER* 5.0 0.2 - - - -
173A GLN* 2.9 23.7 + - - -
174A SER 2.6 30.1 + - - +
175A LEU* 3.2 15.2 - - + +
176A LEU* 2.7 33.1 + - - +
649A ASN* 3.4 26.9 + - - -
650A PRO* 1.4 76.8 + - - +
652A PHE* 1.3 60.8 + - - +
653A VAL* 4.0 0.6 + - - -
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Residues in contact with PHE 652 (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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121A LEU* 4.0 14.2 + - + +
122A PHE* 3.4 25.6 - - + -
123A LEU* 3.2 23.6 + - - +
158A ILE* 5.0 2.8 - - - +
176A LEU* 3.6 33.4 - - + -
478A LEU 5.1 1.1 - - - -
481A PHE* 3.9 14.1 - + - -
482A PHE* 3.4 46.2 - + + -
485A HIS* 3.7 24.7 - + - -
650A PRO* 3.7 26.7 - - + -
651A HIS* 1.3 75.3 - - - +
653A VAL* 1.3 63.9 + - - +
654A ARG* 3.8 16.8 - - - +
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Residues in contact with VAL 653 (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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123A LEU* 3.5 26.5 - - + +
125A ALA* 4.6 6.3 - - + -
155A ILE* 4.0 21.5 - - + -
158A ILE* 4.4 17.5 - - + -
175A LEU* 4.9 3.6 - - + -
176A LEU 2.7 14.8 + - - +
177A ILE* 3.3 34.2 - - + -
178A THR* 3.1 27.7 + - - +
188A ASN* 5.3 1.6 - - + +
651A HIS 4.9 2.7 - - - +
652A PHE* 1.3 77.2 - - - +
654A ARG* 1.4 67.6 + - - +
655A CYS* 4.2 11.7 - - - -
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Residues in contact with ARG 654 (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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122A PHE* 3.3 43.2 - - + -
123A LEU 3.0 9.3 + - - +
124A VAL* 3.5 9.8 - - + +
125A ALA 3.0 23.8 + - - +
176A LEU* 4.1 6.9 + - - +
178A THR* 3.5 24.9 + - - +
478A LEU* 5.7 1.8 + - - +
479A GLN* 3.8 14.3 + - - +
482A PHE* 4.9 9.7 - - - +
652A PHE* 3.8 21.4 - - - +
653A VAL* 1.4 75.2 + - - +
655A CYS* 1.3 63.8 + - - +
656A ILE* 3.7 1.0 + - + +
679A ASN* 3.2 46.4 + - - +
681A VAL* 3.7 17.0 - - + -
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Residues in contact with CYS 655 (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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125A ALA* 3.4 10.1 - - - +
177A ILE* 3.7 29.4 - - - -
178A THR 3.0 12.7 + - - +
179A GLY* 3.5 14.6 - - - -
180A GLU 4.2 0.9 + - - -
183A ALA* 3.4 32.7 - - + +
184A GLY 4.0 6.5 - - - -
185A LYS* 3.9 17.0 - - + -
188A ASN* 4.1 11.2 - - - -
653A VAL* 4.2 8.5 - - - -
654A ARG* 1.3 72.6 - - - +
656A ILE* 1.4 62.5 + - - +
675A GLN* 4.3 1.4 - - - +
679A ASN* 5.2 1.9 + - - -
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Residues in contact with ILE 656 (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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106A LEU* 5.0 1.3 - - + -
124A VAL* 3.3 29.4 - - + -
125A ALA 2.8 11.1 + - - +
126A VAL* 3.5 16.0 - - + -
127A ASN 2.9 28.1 + - - -
183A ALA* 3.9 5.2 - - - +
654A ARG* 4.0 2.5 - - + +
655A CYS* 1.4 74.9 - - - +
657A ILE* 1.3 74.9 + - - +
672A VAL* 4.2 20.9 - - + -
675A GLN* 3.5 23.6 - - + +
676A LEU* 3.2 35.2 - - + -
679A ASN* 4.0 12.1 - - - +
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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