Contacts of the strand formed by residues 70 - 75 (chain A) in PDB entry 4KMR
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 VAL 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A SER* 3.2 13.6 + - - +
69A GLY* 1.3 83.1 - - - +
71A ILE* 1.3 70.4 + - - +
100A VAL* 3.4 21.8 - - + +
102A LEU* 4.0 7.6 - - + -
124A LEU* 3.8 19.3 - - + +
125A THR* 4.2 9.9 - - + -
126A ASP* 2.8 37.5 + - - +
102B LEU* 4.0 23.3 - - + -
124B LEU* 3.8 25.8 - - + -
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Residues in contact with ILE 71 (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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69A GLY 4.3 0.2 - - - -
70A VAL* 1.3 79.4 - - - +
72A GLY* 1.3 62.3 + - - +
90A VAL* 4.5 1.3 - - + -
94A ALA* 4.2 21.1 - - + -
99A LEU* 4.2 24.5 - - + -
100A VAL 3.0 15.1 + - - +
101A VAL* 3.3 14.8 - - + -
102A LEU 2.9 23.7 + - - -
125A THR* 4.0 4.0 - - - -
126A ASP* 5.1 0.2 - - + -
127A GLY 3.5 7.2 - - - +
129A LEU* 4.4 11.0 - - + -
311A VAL* 4.4 19.5 - - + -
314A LEU* 3.9 27.6 - - + -
318A ILE* 3.9 19.1 - - + -
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Residues in contact with GLY 72 (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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71A ILE* 1.3 77.3 - - - +
73A LEU* 1.3 57.2 + - - +
101A VAL* 4.8 0.9 - - - -
102A LEU* 3.3 9.9 - - - -
104A GLU* 6.3 0.2 - - - -
122A LEU* 5.9 1.1 - - - -
125A THR* 3.6 16.0 - - - +
127A GLY 2.9 13.8 + - - -
128A LEU* 3.6 13.4 - - - -
129A LEU* 2.8 34.3 + - - +
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Residues in contact with LEU 73 (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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71A ILE* 6.5 0.2 - - + -
72A GLY* 1.3 73.9 - - - +
74A ALA* 1.3 60.4 + - - +
75A VAL* 3.9 23.6 - - + -
86A LEU* 5.1 2.0 - - + -
87A ALA* 3.7 38.8 - - + +
90A VAL* 4.3 17.9 - - + -
91A ILE* 5.9 0.2 - - + -
101A VAL* 3.9 18.8 - - + -
102A LEU 2.8 7.9 + - - +
103A VAL* 3.4 11.5 - - + +
104A GLU* 2.9 29.2 + - - +
128A LEU* 4.2 0.9 - - - +
129A LEU* 3.4 26.7 - - + +
152A LEU* 4.0 16.4 - - + -
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Residues in contact with ALA 74 (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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73A LEU* 1.3 71.1 - - - +
75A VAL* 1.3 62.3 + - - +
104A GLU* 3.5 13.7 - - + -
106A THR* 4.0 15.3 - - + -
116A ALA* 4.3 10.3 - - + -
128A LEU* 4.1 13.2 - - + +
129A LEU 2.9 10.4 + - - +
130A LEU* 3.8 22.4 - - + +
131A ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 75 (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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73A LEU* 3.9 28.7 - - + -
74A ALA* 1.3 76.9 - - - +
76A PRO* 1.3 76.3 - - + +
77A GLU* 4.1 12.1 - - - +
78A LEU* 4.2 24.9 - - + -
83A PHE* 3.8 28.3 - - + +
86A LEU* 5.5 3.6 - - + -
103A VAL* 4.6 6.5 - - + -
104A GLU 3.1 11.0 + - - +
105A GLN* 3.1 8.2 - - + -
106A THR* 2.9 21.6 + - - -
131A ALA* 4.5 5.6 - - + -
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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