Contacts of the strand formed by residues 88 - 97 (chain A) in PDB entry 1OKM
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 TYR 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A VAL* 3.2 6.2 - - - -
79A LEU* 2.8 42.5 + - + +
84A LEU* 3.9 33.1 - - + +
85A ASP 3.8 22.0 + - - -
86A GLY 3.9 7.0 - - - -
87A THR* 1.3 78.1 - - - +
89A ARG* 1.3 62.6 + - - +
122A HIS* 3.5 17.6 - - + -
123A TRP 3.2 5.6 - - - -
124A ASN* 3.2 40.4 + - + -
139A ASP* 2.9 27.9 + - - +
141A LEU 3.7 10.2 + - - -
142A ALA* 3.4 30.7 - - + -
208A THR* 5.0 2.8 + - - -
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Residues in contact with ARG 89 (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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72A ASP* 2.9 30.1 + - + -
73A SER* 3.6 11.3 + - - +
74A GLN* 3.5 30.6 - - - +
75A ASP* 2.9 29.9 + - - +
77A ALA 3.7 5.2 - - - +
78A VAL* 4.1 6.5 - - + -
88A TYR* 1.3 71.9 - - - +
90A LEU* 1.3 67.9 + - - +
91A ILE 3.4 1.2 + - - -
122A HIS* 2.9 20.9 - - - -
123A TRP* 2.9 50.1 + - - +
125A THR* 3.4 24.6 - - + +
129A GLY 5.3 0.8 + - - -
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Residues in contact with LEU 90 (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 TYR* 4.1 17.0 - - + +
70A PHE* 3.9 47.6 - - + +
71A ASP 4.9 0.7 - - - +
72A ASP* 3.7 15.8 - - - +
77A ALA* 2.9 38.0 + - + +
89A ARG* 1.3 71.4 - - - +
91A ILE* 1.3 59.8 + - - +
92A GLN 3.7 17.5 - - - +
120A LEU* 4.1 14.4 - - + -
121A VAL 3.5 16.8 - - - +
122A HIS* 3.6 24.9 - - + +
181A PRO* 4.5 8.3 - - + -
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Residues in contact with ILE 91 (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 GLU* 3.6 3.6 - - + +
70A PHE* 2.9 29.0 + - - +
72A ASP* 3.7 30.3 - - - +
89A ARG 3.4 0.4 + - - -
90A LEU* 1.3 74.4 - - - +
92A GLN* 1.3 79.4 + - + +
121A VAL* 3.0 27.3 + - + +
123A TRP* 4.0 12.8 - - + -
131A PHE* 3.9 35.7 - - + -
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Residues in contact with GLN 92 (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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67A ASN* 3.9 21.5 + - + -
68A VAL 3.1 17.9 - - - +
69A GLU* 4.3 9.4 - - + -
70A PHE* 4.2 3.1 - - - -
90A LEU* 3.7 6.6 - - - +
91A ILE* 1.3 96.8 - - + +
93A PHE* 1.3 77.4 + - - +
94A HIS* 2.9 35.3 + - - -
121A VAL* 2.9 31.5 + - + +
131A PHE* 6.5 0.2 - - + -
555A SAB 4.0 24.5 + - - -
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Residues in contact with PHE 93 (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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66A PHE* 3.9 1.0 - + - +
67A ASN* 3.5 2.1 - - - -
68A VAL* 3.1 56.3 + - + -
70A PHE* 3.4 39.7 - + - -
90A LEU* 4.9 0.2 - - + -
92A GLN* 1.3 77.5 + - - +
94A HIS* 1.3 63.2 + - - +
95A PHE* 3.7 23.8 - + - -
118A LEU* 3.6 13.9 - - + -
119A HIS 3.0 15.5 - - - +
120A LEU* 3.5 29.8 - - + -
160A VAL* 4.5 5.4 - - + -
179A PHE* 3.6 29.4 - + - -
181A PRO* 4.7 2.5 - - + -
184A LEU* 3.8 12.8 - - + -
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Residues in contact with HIS 94 (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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65A ALA* 4.6 7.4 - - + -
66A PHE 3.5 9.6 - - - +
67A ASN* 3.0 27.0 + - - +
92A GLN* 2.9 22.3 + - - -
93A PHE* 1.3 72.7 - - - +
95A PHE* 1.3 70.1 + - - +
96A HIS* 3.2 14.6 - + - -
118A LEU* 3.4 5.9 - - - +
119A HIS* 2.8 32.3 + - + -
121A VAL* 3.6 19.3 - - + -
262A ZN 2.0 36.9 - - - -
555A SAB 3.1 27.5 + + - -
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Residues in contact with PHE 95 (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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65A ALA* 3.9 8.8 - - - +
66A PHE* 3.6 32.5 + + - -
93A PHE* 3.7 25.4 - + - -
94A HIS* 1.3 78.1 - - - +
96A HIS* 1.3 70.1 + - - +
97A TRP* 3.3 30.8 - - + -
116A ALA* 5.2 1.3 - - + -
117A GLU 3.2 7.9 - - - -
118A LEU* 3.7 38.6 - - + -
148A LEU* 3.8 29.8 - - + -
157A LEU* 3.6 27.6 - - + -
160A VAL* 4.7 0.7 - - + -
184A LEU* 4.6 6.3 - - + -
216A ILE* 5.7 1.3 - - + -
226A PHE* 3.9 10.8 - + + -
244A ASN* 3.9 5.4 + - - -
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Residues in contact with HIS 96 (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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7A TYR* 4.3 9.2 - - - -
64A HIS 6.1 0.2 - - - -
65A ALA* 5.8 3.6 - - + -
94A HIS* 3.2 12.2 - + - -
95A PHE* 1.3 75.2 + - - +
97A TRP* 1.3 60.3 + - - +
104A GLY 3.3 13.7 - - - +
106A GLU* 3.2 28.7 + - + -
116A ALA* 3.0 5.9 - - - +
117A GLU* 2.9 34.7 + - + +
119A HIS* 3.1 21.5 - + - -
199A THR* 3.9 5.2 - - - -
200A THR* 4.3 5.6 - - + -
244A ASN* 2.8 31.0 + - - +
245A TRP* 4.3 0.7 - - + -
262A ZN 2.0 37.7 - - - -
555A SAB 4.1 1.8 - - - -
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Residues in contact with TRP 97 (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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65A ALA* 4.3 3.6 - - + -
66A PHE* 3.8 31.2 - + - -
95A PHE* 3.3 35.9 - - + -
96A HIS* 1.3 74.4 - - - +
98A GLY* 1.3 73.9 + - - +
104A GLY* 3.5 6.9 + - - -
115A ALA 3.7 11.9 - - - +
116A ALA* 3.9 8.1 - - + -
223A VAL* 5.1 5.2 - - + -
226A PHE* 3.5 46.7 + + + -
227A ARG* 3.9 8.2 - - + +
229A LEU* 4.0 1.8 - - + -
241A MET* 2.8 54.7 + - + -
242A VAL* 4.3 2.0 - - - -
243A ASP* 2.9 23.0 + - - -
244A ASN* 2.9 30.1 + - - +
245A TRP* 3.6 1.2 - - - -
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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