Contacts of the helix formed by residues 71 - 79 (chain M) in PDB entry 7KHI
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 71 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678C ARG* 4.0 11.6 + - - -
681C MET* 5.0 2.4 - - - +
814C ASP* 5.1 1.6 - - - +
1073C LYS* 5.4 5.1 + - - -
1106C ARG* 4.4 14.3 + - - +
460D ASP* 5.2 4.0 - - - +
462D ASP* 4.1 19.4 - - - +
69M PHE* 3.3 2.6 - - - +
70M PRO* 1.3 81.0 - - + +
72M PRO* 1.3 81.2 - - - +
73M VAL* 3.3 26.5 - - - +
74M ASP* 3.0 38.6 + - - +
75M ARG* 3.2 9.0 + - - +
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Residues in contact with PRO 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783D LEU* 4.0 14.4 - - + +
786D THR* 4.2 15.9 - - + +
70M PRO 4.0 5.4 - - - +
71M ASP* 1.3 94.1 - - - +
73M VAL* 1.3 55.9 + - + +
74M ASP 3.3 1.7 + - - -
75M ARG* 4.1 6.3 - - + -
76M ALA* 3.8 14.2 + - - +
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Residues in contact with VAL 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565C GLU* 4.5 5.2 - - - +
677C ASN* 4.1 30.8 - - + +
678C ARG* 3.4 32.7 + - - +
681C MET* 3.4 41.7 - - + -
783D LEU* 4.5 13.9 - - + -
71M ASP* 3.3 19.5 + - - +
72M PRO* 1.3 78.8 - - + +
74M ASP* 1.3 58.1 + - - +
76M ALA* 4.5 3.4 - - - -
77M ALA* 4.1 10.9 + - - +
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Residues in contact with ASP 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C ARG* 3.7 20.4 + - - +
1105C SER* 5.8 3.8 - - - +
1106C ARG* 5.0 5.0 + - + -
731D ARG* 4.1 19.3 + - - +
69M PHE* 2.9 34.3 - - - +
70M PRO* 5.1 2.4 - - - +
71M ASP* 3.0 22.3 + - + +
73M VAL* 1.3 80.2 - - - +
75M ARG* 1.3 65.0 + - - +
76M ALA 3.2 1.1 - - - -
77M ALA* 3.4 11.1 - - + +
78M GLN* 2.9 29.3 + - - +
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Residues in contact with ARG 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D THR* 4.6 11.9 - - + +
789D LYS* 2.9 32.9 - - - +
928D THR* 2.1 41.1 + - + +
929D GLN* 3.0 23.8 + - - +
930D LEU 4.1 2.2 + - - -
67M ALA 4.3 10.0 + - - -
68M ASN* 5.5 1.2 - - - +
69M PHE* 3.8 32.8 - - + +
71M ASP 3.2 12.6 + - - +
72M PRO* 4.4 7.0 - - + +
74M ASP* 1.3 84.2 + - - +
76M ALA* 1.3 57.0 + - - +
78M GLN* 3.4 11.2 + - - +
79M GLU* 2.9 65.2 + - - +
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Residues in contact with ALA 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677C ASN* 5.1 6.7 - - - +
779D ALA 5.3 0.2 - - - +
782D GLY* 3.9 1.4 - - - +
783D LEU* 3.7 33.0 - - + +
786D THR* 3.3 24.1 + - - +
72M PRO 3.8 13.3 + - - +
73M VAL 4.8 4.0 - - - +
74M ASP 3.2 0.6 - - - -
75M ARG* 1.3 75.6 - - - +
77M ALA* 1.3 64.3 + - - +
79M GLU* 3.4 6.2 - - - +
80M GLU* 2.9 29.0 + - - +
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Residues in contact with ALA 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675C ASP* 5.0 7.9 - - - +
677C ASN* 4.8 12.7 - - + +
678C ARG* 6.1 1.3 - - - +
1105C SER 5.9 2.5 - - - +
1107C MET* 5.1 16.4 - - + +
73M VAL 4.1 6.3 + - - +
74M ASP* 3.2 23.0 + - + +
76M ALA* 1.3 81.2 - - - +
78M GLN* 1.3 59.5 + - - +
79M GLU 3.4 0.2 + - - -
80M GLU* 3.5 11.0 + - - +
81M GLU* 4.0 11.1 + - - +
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Residues in contact with GLN 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736D GLN* 5.3 12.8 - - - +
929D GLN 5.7 2.0 + - - -
65M GLU* 4.8 5.8 - - + +
66M ALA* 4.2 22.8 - - - +
67M ALA 4.7 2.5 + - - +
69M PHE* 3.3 40.5 - - + -
74M ASP 2.9 10.1 + - - +
75M ARG* 3.5 28.4 + - - +
77M ALA* 1.3 75.8 - - - +
79M GLU* 1.3 57.2 + - - +
80M GLU 3.5 1.0 + - - -
81M GLU* 4.3 5.5 - - - +
82M PHE* 2.8 49.9 + - + -
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Residues in contact with GLU 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782D GLY* 4.1 12.0 - - - +
785D ASP* 3.8 20.5 - - - +
786D THR* 3.9 16.8 + - - -
789D LYS* 4.5 8.2 + - - +
931D THR* 4.4 21.2 + - - +
932D MET* 4.9 4.3 + - - +
75M ARG* 2.9 41.7 + - - +
76M ALA* 3.2 5.0 + - - -
78M GLN* 1.3 76.6 - - - +
80M GLU* 1.3 61.4 + - - +
81M GLU 3.7 0.7 - - - -
82M PHE* 4.3 12.3 - - + -
83M SER* 4.0 16.0 + - - +
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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