Contacts of the strand formed by residues 70 - 79 (chain N) in PDB entry 1MMJ
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 70 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55N VAL 3.9 0.9 - - - +
56N VAL* 3.5 1.9 - - - -
57N VAL* 2.8 57.1 + - + +
68N THR 3.8 4.4 + - - +
69N GLU* 1.4 75.2 - - - +
71N TYR* 1.4 64.1 - - - +
72N VAL* 4.3 6.3 + - + +
103N VAL* 3.4 18.2 - - + +
104N THR* 3.0 48.4 + - - +
106N ASN* 4.6 4.9 + - - -
109N VAL* 3.9 13.9 - - - +
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Residues in contact with TYR 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N ARG* 3.6 41.2 + - - +
55N VAL 3.7 3.6 - - - -
56N VAL* 3.8 28.3 - - + -
59N GLU* 4.9 4.1 + - - -
69N GLU* 3.9 33.7 + - + +
70N GLN* 1.4 77.4 - - - +
72N VAL* 1.4 66.3 + - - +
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Residues in contact with VAL 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N ARG* 4.4 5.8 - - - +
55N VAL* 2.8 49.6 + - + +
57N VAL* 5.4 0.2 - - + -
70N GLN* 4.4 7.6 - - + +
71N TYR* 1.4 85.6 - - - +
73N GLY* 1.3 64.9 + - - +
99N LEU* 4.0 23.1 - - + -
100N ALA* 5.5 0.2 - - + -
101N GLN* 4.6 17.3 - - + +
102N SER 5.8 0.4 - - - -
103N VAL* 3.9 28.0 - - + +
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Residues in contact with GLY 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N PHE 4.3 7.0 - - - -
54N ARG* 4.5 4.5 - - - -
72N VAL* 1.3 76.4 - - - +
74N VAL* 1.4 63.3 + - - +
99N LEU* 3.4 5.0 - - - +
100N ALA* 2.8 38.0 + - - +
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Residues in contact with VAL 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N PHE* 3.5 39.8 + - + +
54N ARG* 4.1 0.9 - - - -
55N VAL* 3.8 28.5 - - + -
73N GLY* 1.4 73.0 - - - -
75N GLN* 1.3 62.2 + - - +
76N LYS 4.1 5.2 - - - +
77N ILE* 4.0 30.1 - - + -
97N LEU* 4.1 22.9 - - + -
98N ARG 3.8 4.5 - - - +
99N LEU* 4.4 2.9 - - + +
100N ALA* 5.1 0.7 - - - -
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Residues in contact with GLN 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N VAL* 1.3 74.1 - - - +
76N LYS* 1.4 59.8 + - + +
98N ARG* 2.7 53.5 + - - +
99N LEU 3.4 15.9 + - - -
100N ALA* 3.7 25.8 + - + +
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Residues in contact with LYS 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N VAL* 3.6 4.1 - - - +
75N GLN* 1.4 81.8 - - + +
77N ILE* 1.4 70.2 - - - +
78N VAL* 3.9 23.8 - - + -
96N LEU 3.8 0.3 - - - +
97N LEU* 3.4 3.6 - - - -
98N ARG* 2.8 82.6 + - + +
240N ASN* 3.1 16.6 + - - -
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Residues in contact with ILE 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N VAL* 3.5 40.4 - - + +
53N PHE* 4.2 25.6 - - + -
74N VAL* 4.0 17.7 - - + -
76N LYS* 1.4 81.4 - - - +
78N VAL* 1.4 60.9 + - - +
79N VAL* 4.0 16.2 + - + +
95N ALA* 4.9 0.2 - - + -
96N LEU 3.5 4.0 - - - +
97N LEU* 4.0 10.1 - - + -
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Residues in contact with VAL 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N TRP* 4.7 4.7 - - + -
76N LYS* 3.9 27.6 - - + -
77N ILE* 1.4 72.2 - - - +
79N VAL* 1.4 67.5 + - - +
81N PRO* 6.0 0.9 - - + -
95N ALA* 3.2 4.8 - - - +
96N LEU* 2.8 41.4 + - + +
232N TRP* 4.0 9.8 - - + +
236N VAL* 3.9 42.8 - - + -
240N ASN 4.3 7.2 - - - +
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Residues in contact with VAL 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N ALA* 3.6 13.7 - - + +
47N VAL* 4.2 11.4 - - + +
48N ASP* 5.2 3.1 - - - +
77N ILE* 4.0 23.2 + - + +
78N VAL* 1.4 79.7 - - - +
80N HIS* 1.3 71.3 + - - +
81N PRO* 3.2 7.1 - - - +
83N TRP* 3.6 35.2 - - + -
95N ALA* 4.0 10.5 - - + -
232N TRP* 4.0 2.9 - - - -
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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