Contacts of the strand formed by residues 71 - 82 (chain A) in PDB entry 1K89
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A PRO* 4.8 9.4 - - + -
64A TRP 3.5 9.6 - - - +
65A GLU* 4.5 12.1 - - + +
69A GLY 4.2 7.6 - - - +
70A LYS* 1.3 92.0 - - - +
72A HIS* 1.3 71.4 + - - +
73A VAL* 4.9 7.4 - - + +
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Residues in contact with HIS 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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63A PRO* 3.2 4.0 - - - +
64A TRP* 2.8 76.4 + + + +
66A ASP* 2.8 28.4 + - + +
70A LYS* 3.2 43.4 + - + +
71A VAL* 1.3 74.8 + - - +
73A VAL* 1.3 65.4 + - - +
74A ASN* 4.5 2.5 - - - +
135A LYS* 6.3 1.3 - - - -
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Residues in contact with VAL 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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61A ARG* 3.8 32.3 - - + -
62A VAL 3.5 6.7 - - - +
63A PRO* 4.4 8.1 - - + -
71A VAL* 4.9 8.5 - - + +
72A HIS* 1.3 81.9 - - - +
74A ASN* 1.3 73.2 + - - +
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Residues in contact with ASN 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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61A ARG* 3.6 2.6 - - - -
62A VAL* 2.7 40.4 + - - +
64A TRP* 2.9 29.6 + - - -
72A HIS* 4.5 1.6 - - - +
73A VAL* 1.3 85.9 + - - +
75A THR* 1.3 61.4 + - - +
128A SER* 3.7 11.4 - - - +
129A ASP* 3.0 25.2 + - - +
130A PHE* 3.5 24.4 - - - +
131A ASP 5.0 0.6 - - - +
143A PHE* 4.1 7.2 - - + -
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Residues in contact with THR 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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59A GLU* 4.4 12.6 - - + +
60A PHE 3.5 10.8 - - - +
61A ARG* 4.9 1.1 - - - +
62A VAL* 4.2 1.1 - - - -
74A ASN* 1.3 78.8 + - - +
76A GLY* 1.3 69.9 + - - +
77A TYR* 3.8 28.4 - - + +
128A SER* 2.7 32.0 + - - -
129A ASP* 3.1 19.4 + - - -
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Residues in contact with GLY 76 (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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59A GLU* 3.0 5.4 - - - -
60A PHE* 2.7 51.8 + - - -
62A VAL* 3.7 3.6 - - - +
75A THR* 1.3 76.7 - - - +
77A TYR* 1.3 63.0 + - - -
127A GLY 3.4 6.7 - - - -
147A PHE* 3.8 16.8 - - - -
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Residues in contact with TYR 77 (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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57A VAL* 5.8 0.2 - - + -
58A ILE 3.3 7.2 - - - -
59A GLU* 3.5 38.9 + - + -
60A PHE* 4.0 5.2 - - - -
75A THR* 3.8 33.6 - - + +
76A GLY* 1.3 75.0 - - - -
78A ARG* 1.3 64.4 - - - +
79A VAL* 5.3 0.9 - - + -
92A LEU* 4.8 0.5 - - - +
98A VAL* 3.7 32.0 + - + -
99A ASN* 3.9 11.3 - - - +
100A LEU* 3.8 28.5 + - + -
103A MET* 3.9 27.1 - - + -
126A GLY* 3.1 1.4 - - - -
127A GLY 2.8 31.7 + - - +
129A ASP* 4.9 4.4 + - - -
147A PHE* 4.6 5.5 - - - -
151A LEU* 5.3 0.3 - - - +
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Residues in contact with ARG 78 (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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57A VAL* 3.6 0.9 - - - -
58A ILE* 2.8 50.0 + - + +
77A TYR* 1.3 75.1 - - - +
79A VAL* 1.3 63.1 + - - +
80A GLN* 3.8 14.2 + - + +
90A GLY 3.0 41.8 + - - +
91A GLY 3.3 4.0 + - - -
92A LEU* 3.7 13.7 - - - +
124A ALA* 3.8 12.7 - - - +
125A LYS* 3.4 9.1 - - - +
126A GLY* 3.3 24.7 - - - +
151A LEU* 4.1 24.7 - - + -
160A ASP* 2.6 45.1 + - - +
162A PRO* 3.6 17.2 - - - +
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Residues in contact with VAL 79 (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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54A PRO* 3.9 18.6 - - + -
56A ARG 3.8 3.1 - - - -
57A VAL* 4.3 7.6 - - + +
77A TYR* 5.3 1.1 - - + -
78A ARG* 1.3 76.1 - - - +
80A GLN* 1.3 59.7 + - - +
81A PHE* 3.4 30.8 + - + -
100A LEU* 3.9 22.4 - - + -
103A MET* 3.6 35.4 - - + +
104A LYS* 4.3 6.7 - - + +
107A GLY* 5.3 0.7 - - - -
124A ALA* 3.1 22.2 - - - +
125A LYS 2.9 17.7 + - - +
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Residues in contact with GLN 80 (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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54A PRO* 3.9 0.4 - - - -
55A GLU* 3.1 5.2 + - - +
56A ARG* 2.7 77.5 + - + +
58A ILE* 4.0 11.5 - - - +
78A ARG* 4.0 12.8 - - + +
79A VAL* 1.3 70.9 - - - +
81A PHE* 1.3 62.6 + - - +
82A ASN 3.7 1.1 - - - -
88A TYR* 3.7 31.8 - - + -
124A ALA* 4.0 5.4 - - + -
154A HIS* 3.0 27.6 + - - +
159A ILE* 4.9 0.8 - - - +
160A ASP* 2.9 33.1 + - - +
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.8 15.9 - + - -
51A MET 3.3 26.4 - - - +
52A VAL 3.6 15.9 - - - -
53A ILE 4.3 1.4 - - - +
54A PRO* 3.6 35.3 - - + +
55A GLU* 3.1 22.6 + - - +
79A VAL* 3.4 18.4 + - + +
80A GLN* 1.3 74.9 - - - +
82A ASN* 1.3 68.2 + - + +
104A LYS* 3.5 26.5 - - + -
107A GLY 3.6 15.9 - - - +
108A PHE* 3.5 31.6 - + + -
111A ALA* 5.1 2.0 - - + -
123A GLY 3.1 14.1 + - - +
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Residues in contact with ASN 82 (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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51A MET* 4.7 16.6 + - - +
55A GLU* 3.6 8.5 + - - +
80A GLN 3.7 0.4 - - - -
81A PHE* 1.3 85.1 + - + +
83A GLY* 1.3 58.6 + - - +
84A ALA* 3.1 34.0 + - - +
85A ILE 4.9 0.2 + - - -
88A TYR* 3.6 5.7 - - - -
111A ALA* 4.1 20.1 - - + +
122A GLY* 3.2 2.8 - - - -
123A GLY 2.7 32.0 + - - -
438A ILE* 3.7 29.9 - - + +
442A MET* 3.8 16.1 - - - +
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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