Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 4KM9
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 HIS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ARG* 3.9 3.2 - - - +
76A ASN* 2.9 61.2 + - + +
78A GLY* 4.2 1.8 - - - -
84A ILE* 4.5 0.2 - - + -
85A PRO 2.9 24.0 + - - -
86A GLU* 1.3 76.0 - - - +
88A TRP* 1.3 69.8 + - - +
89A HIS* 4.6 1.6 - - + -
123A ARG* 3.0 50.4 + - + -
124A LEU 3.2 14.4 - - - +
126A ARG* 3.8 5.3 - - - +
233A TRP* 4.1 10.5 - + - -
235A ILE* 3.4 33.1 - - + +
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Residues in contact with TRP 88 (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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74A TYR 3.6 12.1 - - - +
75A ARG* 3.7 46.9 - - + -
87A HIS* 1.3 74.1 - - - +
89A HIS* 1.3 60.0 + - - +
90A TYR* 3.4 22.8 - - + +
122A PHE 3.5 1.4 - - - +
123A ARG* 3.3 6.1 - - - -
124A LEU* 2.7 48.8 + - + +
126A ARG* 3.7 24.1 - - + +
130A GLU* 2.6 37.4 + - + -
131A SER 4.2 2.5 - - - -
132A ALA* 3.6 28.3 - - - -
133A PRO* 3.6 29.4 - - + -
134A PRO* 3.6 16.6 - - + +
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Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.3 15.0 - - + -
45A TYR* 2.7 31.7 + + + +
72A SER 3.8 0.3 - - - +
73A MET* 3.3 4.2 - - - -
74A TYR* 2.7 47.6 + - + +
75A ARG 5.0 0.2 - - - +
76A ASN* 5.1 1.6 - - + -
87A HIS* 3.8 6.1 + - + -
88A TRP* 1.3 72.8 - - - +
90A TYR* 1.3 83.8 + - - +
91A ILE* 4.0 15.5 - - + +
121A THR* 3.7 8.8 - - - +
122A PHE 3.5 8.7 - - - -
123A ARG* 3.2 38.5 + - + +
182A ASP* 3.4 18.9 + - - -
185A MET* 4.5 2.2 - - + -
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Residues in contact with TYR 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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71A VAL* 4.5 8.3 - - + -
72A SER 3.4 4.3 - - - +
73A MET* 3.7 30.1 - - + -
88A TRP* 3.4 32.2 - - + +
89A HIS* 1.3 76.8 - - - +
91A ILE* 1.3 66.5 + - - +
121A THR* 3.0 26.4 - - - -
122A PHE* 2.9 34.6 + + + +
124A LEU* 4.3 4.6 - - + +
133A PRO* 3.4 14.1 - - + +
134A PRO* 2.6 44.1 + - - +
137A PRO* 3.6 25.6 - - + +
138A ALA 4.5 4.0 - - - -
141A MET* 4.0 17.5 - - - -
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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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37A ILE* 4.1 16.8 - - + -
41A CYS* 3.6 26.2 - - + -
45A TYR* 5.0 3.4 - - + -
71A VAL* 3.3 4.8 - - - +
72A SER* 3.0 36.7 + - - +
74A TYR* 4.0 18.6 - - + -
89A HIS* 4.0 20.0 - - + +
90A TYR* 1.3 79.2 - - - +
92A SER* 1.3 72.0 + - - +
93A PHE* 3.8 12.3 - - + -
119A GLU* 5.4 0.2 - - + -
120A LEU 3.6 6.7 - - - +
121A THR* 3.7 17.3 - - + -
141A MET* 4.0 3.6 - - - -
185A MET* 4.3 16.2 - - + -
197A PHE* 5.0 2.9 - - + -
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Residues in contact with SER 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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37A ILE* 4.5 0.7 - - - +
68A LEU* 3.7 26.6 - - - +
70A TYR 3.6 4.9 - - - -
71A VAL* 4.6 1.3 - - - +
91A ILE* 1.3 76.9 - - - +
93A PHE* 1.3 72.7 + - - +
95A LEU* 4.4 0.9 - - - +
119A GLU* 2.6 38.8 + - - +
120A LEU* 3.0 30.9 + - - +
141A MET* 3.5 19.5 - - - +
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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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34A LEU* 4.1 21.5 - - + -
37A ILE* 3.3 39.3 - - + -
38A TYR* 4.1 14.4 - + + -
41A CYS* 4.5 6.3 - - - -
53A GLN* 5.0 1.3 - - - -
68A LEU* 3.4 6.0 - - - +
69A ASP* 2.8 27.4 + - - -
70A TYR* 2.9 42.5 + + + +
72A SER* 3.4 26.7 - - - -
91A ILE* 3.8 16.6 - - + -
92A SER* 1.3 80.1 - - - +
94A GLY* 1.3 58.6 + - - +
95A LEU 3.9 0.4 - - - -
98A LEU* 3.8 24.9 - - + -
119A GLU* 3.4 4.7 - - - -
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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