Contacts of the strand formed by residues 89 - 98 (chain C) in PDB entry 5HK1
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 TRP 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C VAL* 3.7 33.0 - - + -
85C ASN* 3.6 6.1 + - - -
86C ALA* 3.1 52.9 + - + -
87C GLY 3.3 0.8 - - - -
88C GLY* 1.3 80.8 - - - +
90C MET* 1.3 72.5 + - - +
107C PHE* 3.7 17.9 - + - -
113C SER* 3.1 15.0 - - - +
114C ARG 3.5 11.0 - - - +
115C GLY* 3.9 14.8 - - - -
116C HIS 2.8 30.1 + - - -
117C SER* 4.5 1.6 - - - +
162C VAL* 4.2 2.5 - - + +
164C TRP* 3.5 33.1 - + + -
184C PHE* 4.0 11.8 - + - -
185C ALA* 5.8 0.7 - - - -
188C ASP* 4.3 0.9 - - - +
301C 61W 3.5 37.0 - + + -
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Residues in contact with MET 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLY* 3.4 33.0 - - - +
116A HIS* 3.5 25.8 - - + -
136A TRP* 4.8 1.8 - - + -
160A THR 4.3 0.4 - - - +
161A ALA* 3.7 26.2 - - + +
83C PHE* 3.6 35.2 - - + -
84C VAL 3.3 5.8 - - - +
85C ASN* 3.3 26.9 - - - +
89C TRP* 1.3 77.9 - - - +
91C GLY* 1.3 64.7 + - - +
107C PHE* 5.1 0.2 - - - -
109C THR* 3.9 11.4 + - - +
112C GLY 4.8 0.2 - - - +
113C SER* 2.9 24.9 + - - +
164C TRP* 5.2 0.7 - - - -
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Residues in contact with GLY 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TRP* 4.1 11.7 - - - -
83C PHE* 3.3 9.7 - - - -
84C VAL 2.6 37.2 + - - +
89C TRP* 4.1 2.2 - - - -
90C MET* 1.3 75.5 - - - +
92C ALA* 1.3 56.7 + - - -
107C PHE* 3.8 16.4 - - - -
108C GLY 3.4 11.2 - - - -
109C THR* 4.2 1.3 - - - -
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TRP* 3.5 25.8 - - + -
140A THR 5.6 1.1 - - - +
81C TRP* 3.4 23.4 - - + -
82C VAL 3.6 11.4 - - - +
83C PHE* 4.1 9.9 - - + +
84C VAL* 4.2 0.4 - - - +
91C GLY* 1.3 74.3 - - - +
93C MET* 1.3 59.7 + - - +
107C PHE* 3.2 9.2 - - - -
108C GLY 2.8 29.9 + - - +
169C TRP* 5.0 0.2 - - + -
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Residues in contact with MET 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLN 3.3 2.9 - - - +
81C TRP* 3.4 6.8 - - - -
82C VAL* 2.9 55.0 + - + +
84C VAL* 3.5 23.7 - - + +
92C ALA* 1.3 74.3 - - - +
94C CYS* 1.3 59.8 + - - +
95C LEU* 3.9 21.5 - - + +
105C LEU* 4.3 11.7 - - + -
106C LEU 3.1 9.4 - - - +
107C PHE* 4.2 7.9 - - + -
202C THR* 4.1 24.9 - - + +
205C SER* 4.2 18.8 - - - -
301C 61W 4.1 28.5 - - + +
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Residues in contact with CYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ILE* 5.7 0.4 - - - -
79C LEU* 3.9 25.8 - - - -
80C GLN 3.8 28.3 - - - +
81C TRP* 3.7 29.1 - - + -
93C MET* 1.3 74.3 - - - +
95C LEU* 1.3 65.2 + - - +
96C LEU* 3.4 11.1 + - - +
105C LEU* 3.3 3.5 - - - -
106C LEU* 2.8 43.6 + - + -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 3.3 20.7 - - + +
78C GLU 5.0 1.4 - - - +
79C LEU* 3.5 13.3 - - - +
80C GLN 4.6 3.1 + - - +
93C MET* 3.9 12.7 - - + +
94C CYS* 1.3 72.1 - - - +
96C LEU* 1.3 60.7 + - - +
97C HIS 3.4 22.9 - - - +
98C ALA* 3.6 23.1 - - + -
103C TYR* 4.5 5.4 - - + -
104C VAL 3.5 8.5 - - - +
105C LEU* 4.1 17.9 - - + -
205C SER* 3.3 47.4 + - - +
206C TYR* 3.8 5.4 - - - +
301C 61W 4.6 15.9 - - + -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 5.0 2.0 - - + -
62C ILE* 3.8 33.7 - - + -
65C LEU* 4.1 25.4 - - + -
72C HIS 3.9 0.2 - - - +
73C VAL* 3.6 13.9 - - + -
74C LEU* 3.0 33.2 + - - +
79C LEU* 3.8 24.7 - - + -
94C CYS* 3.9 17.0 - - - +
95C LEU* 1.3 75.5 - - - +
97C HIS* 1.3 62.9 + - + +
104C VAL* 2.9 24.1 + - + +
106C LEU* 3.9 28.3 - - + +
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Residues in contact with HIS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 4.2 7.0 - - + -
37C PHE* 3.8 22.9 - + + -
72C HIS* 2.8 32.2 + - + +
73C VAL* 5.2 1.6 - - + -
74C LEU* 5.2 2.5 - - - -
95C LEU* 3.4 5.1 - - - +
96C LEU* 1.3 79.7 - - + +
98C ALA* 1.3 70.6 + - - +
99C SER* 4.4 5.7 + - - -
102C GLU* 3.9 25.1 + - + +
103C TYR* 3.2 15.1 - - - -
104C VAL* 2.8 45.0 + - + +
209C GLY* 5.4 0.4 - - - -
213C GLU* 3.2 38.4 + - + -
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 3.6 29.2 - - + -
97C HIS* 1.3 83.1 + - - +
99C SER* 1.3 61.6 + - - +
102C GLU 3.5 6.7 - - - -
103C TYR* 4.1 5.2 - - + +
206C TYR* 3.7 20.9 - - + -
209C GLY* 3.2 36.5 - - - +
210C LEU 3.5 0.9 + - - -
213C GLU* 4.4 3.2 + - - +
301C 61W 4.6 1.6 - - + -
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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