Contacts of the strand formed by residues 90 - 106 (chain H) in PDB entry 5HK5
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 ARG 90 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H THR* 3.8 0.7 - - - -
82H VAL* 2.9 36.1 + - + +
88H ARG* 3.7 1.5 + - - +
89H SER* 1.3 76.4 - - - +
91H THR* 1.3 73.0 + - - +
92H ILE* 3.8 9.5 + - + +
133H VAL* 4.7 17.4 - - + +
134H GLU 3.9 21.5 - - - +
135H LEU* 4.8 14.6 - - + +
136H GLU* 4.3 12.5 + - - +
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Residues in contact with THR 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ARG* 4.3 23.8 - - + +
80H GLN 3.4 10.8 - - - +
81H THR* 4.4 10.8 + - - +
89H SER* 4.5 0.4 + - - -
90H ARG* 1.3 83.2 + - - +
92H ILE* 1.3 72.9 + - - +
93H LEU* 6.0 0.9 - - + -
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Residues in contact with ILE 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ARG* 3.7 1.4 - - - -
80H GLN* 2.8 77.1 + - + +
82H VAL* 3.5 22.0 - - + -
90H ARG* 3.8 11.6 + - + +
91H THR* 1.3 82.7 - - - +
93H LEU* 1.3 62.1 + - - +
94H ASN* 4.2 8.5 - - + +
131H VAL* 6.2 0.9 - - + -
133H VAL* 3.8 28.7 - - + -
149H ILE* 4.7 9.6 - - + -
151H LYS* 6.0 2.7 - - + -
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Residues in contact with LEU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H PRO* 4.8 13.5 - - + -
78H LEU 3.9 12.8 - - - +
79H ARG* 3.8 32.8 - - + +
91H THR* 6.0 1.3 - - + -
92H ILE* 1.3 77.7 - - - +
94H ASN* 1.3 66.6 + - - +
95H ARG* 4.9 12.1 + - - +
151H LYS* 3.6 21.0 + - - +
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Residues in contact with ASN 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G PRO* 3.9 13.8 - - - +
77H PRO* 4.0 3.1 - - - +
78H LEU* 2.8 34.8 + - + +
80H GLN* 2.7 33.2 + - + +
92H ILE* 3.8 4.9 + - + +
93H LEU* 1.3 79.0 - - - +
95H ARG* 1.3 87.3 + - - +
149H ILE* 4.0 5.1 - - - +
150H GLN 2.9 26.0 + - - -
151H LYS* 3.5 13.7 - - - +
152H VAL 3.3 22.5 + - - -
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Residues in contact with ARG 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G PRO* 3.3 25.1 - - - +
75H THR* 2.7 42.9 - - - +
76H GLN 3.1 14.7 + - - +
77H PRO* 5.1 5.7 - - + +
78H LEU* 4.1 5.6 - - - -
93H LEU* 4.9 11.1 + - - +
94H ASN* 1.3 86.8 + - - +
96H PHE* 1.3 60.4 + - - +
151H LYS* 3.9 21.0 - - - +
152H VAL* 3.6 30.2 + - + +
153H LYS* 4.5 9.3 - - - +
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Residues in contact with PHE 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G VAL* 3.4 43.5 - - + -
63G THR* 3.8 21.8 - - + -
104G PHE* 4.3 14.4 - + - -
105G TYR 3.3 13.5 - - - +
106G ILE* 4.2 14.6 - - + -
107G PRO* 4.5 0.2 - - - -
75H THR* 3.5 3.5 - - - -
76H GLN* 2.8 61.6 + - + +
77H PRO 3.5 12.3 - - - -
78H LEU* 4.1 13.0 - - + -
95H ARG* 1.3 73.5 - - - +
97H CYS* 1.3 74.8 + - - +
98H TYR* 3.8 22.4 - + + -
152H VAL* 5.0 0.7 - - - -
155H CYS* 4.6 0.4 - - - -
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Residues in contact with CYS 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PHE* 3.2 6.7 - - - -
105G TYR* 2.8 33.7 + - + +
74H LYS 3.6 0.2 - - - -
96H PHE* 1.3 80.6 - - - +
98H TYR* 1.3 61.0 + - - +
123H CYS* 3.6 20.9 - - - +
124H LYS 3.7 0.2 - - - -
125H PRO* 3.6 26.2 - - - -
152H VAL* 3.8 11.9 - - - -
155H CYS* 2.0 49.8 - - + -
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Residues in contact with TYR 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G TYR 3.9 22.2 - - - -
68G LEU* 3.7 8.4 - - + -
69G LYS* 2.8 31.1 + - + +
102G ASN* 2.6 40.0 + - + -
103G SER 3.5 5.6 - - - -
104G PHE* 3.2 29.8 - + + -
72H TRP* 3.3 32.3 - + - -
74H LYS* 3.0 29.9 + - - +
76H GLN* 4.4 15.4 - - + +
96H PHE* 3.8 20.1 + + + -
97H CYS* 1.3 75.8 - - - +
99H GLY* 1.3 68.0 + - - +
123H CYS* 3.5 3.6 - - - -
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Residues in contact with GLY 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CYS 3.8 0.3 - - - +
102G ASN* 3.3 5.9 - - - +
103G SER* 3.0 32.4 + - - -
72H TRP* 3.2 21.8 - - - -
73H CYS* 3.7 5.2 - - - -
98H TYR* 1.3 77.7 - - - +
100H GLN* 1.3 63.6 + - - +
101H CYS* 4.0 1.3 - - - -
123H CYS* 3.5 11.4 - - - -
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Residues in contact with GLN 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LYS* 3.3 30.0 + - - +
70G SER 3.0 33.6 + - - +
71G ASP* 3.5 6.5 - - - +
72G TRP* 4.7 2.8 + - - -
100G GLN* 4.0 30.2 - - + +
101G CYS 3.5 5.4 - - - +
102G ASN* 3.2 32.2 + - - +
71H ASP* 3.8 4.0 - - - -
72H TRP* 2.9 57.3 + - + +
99H GLY* 1.3 70.3 - - - -
101H CYS* 1.3 61.4 + - - +
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Residues in contact with CYS 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G GLY 3.8 0.3 - - - +
100G GLN* 3.3 16.7 - - - -
101G CYS* 3.4 13.1 + - - +
103G SER* 5.1 2.0 - - - -
71H ASP* 3.6 2.2 - - - +
72H TRP 4.5 0.2 - - - -
99H GLY 4.6 1.1 - - - -
100H GLN* 1.3 75.2 - - - +
102H ASN* 1.3 65.3 + - - +
103H SER* 4.3 3.1 - - - -
121H ALA* 3.6 23.5 - - + +
122H PHE 4.0 2.5 - - - +
123H CYS* 3.8 26.7 - - - -
157H CYS* 2.0 55.4 - - + -
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Residues in contact with ASN 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G TYR* 2.6 33.3 + - + -
99G GLY 3.4 4.0 - - - -
100G GLN* 2.9 18.1 + - - +
68H LEU* 5.3 7.1 - - - +
69H LYS 2.9 19.3 + - - -
70H SER* 4.8 0.2 - - - +
71H ASP* 2.8 32.9 + - - +
101H CYS* 1.3 76.7 - - - +
103H SER* 1.3 58.9 + - - +
104H PHE* 4.1 13.5 - - + -
119H SER* 4.5 1.7 + - - -
121H ALA* 3.3 17.7 - - - +
159H SER* 5.1 2.1 - - - -
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Residues in contact with SER 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G TYR* 3.4 8.3 - - - -
99G GLY 2.9 34.1 + - - -
101G CYS* 5.1 2.7 - - - -
121G ALA 4.5 5.4 - - - -
122G PHE* 3.4 6.7 - - - -
123G CYS* 3.2 28.2 + - - +
101H CYS 4.3 4.0 - - - -
102H ASN* 1.3 78.5 - - - +
104H PHE* 1.3 63.9 + - - +
118H GLN* 3.9 0.9 + - - -
119H SER* 2.8 31.7 + - - -
121H ALA* 4.8 1.1 - - - -
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Residues in contact with PHE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G PHE* 4.4 13.2 - + + -
97G CYS 3.3 7.0 - - - +
98G TYR* 3.2 42.8 - + + -
123G CYS 4.2 1.3 - - - -
62H VAL* 5.6 4.3 - - + -
63H THR* 5.8 1.8 - - + -
68H LEU* 4.1 26.5 - - + -
102H ASN* 4.1 20.6 - - + -
103H SER* 1.3 76.1 + - - +
105H TYR* 1.3 62.0 + - - +
106H ILE* 4.8 7.9 - - + -
117H PHE* 3.7 17.7 - + + +
118H GLN* 3.3 11.4 + - - -
119H SER* 2.9 40.7 + - - +
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Residues in contact with TYR 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PHE* 3.0 9.2 - - - +
97G CYS* 2.8 52.6 + - + +
123G CYS 4.0 2.5 - - - +
125G PRO* 3.7 25.2 - - + +
128G VAL* 6.0 0.9 - - - +
150G GLN* 4.5 14.7 + - - -
152G VAL* 3.7 26.5 - - + -
104H PHE* 1.3 73.7 - - - +
106H ILE* 1.3 62.4 + - - +
107H PRO* 3.7 20.8 - - + +
108H ARG 4.8 0.7 + - - -
116H SER* 3.6 32.7 + - - -
117H PHE 3.2 12.1 - - - -
118H GLN* 3.3 31.0 - - + +
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G LEU* 4.0 11.0 - - + -
96G PHE* 4.1 6.1 - - + -
60H LEU* 3.9 24.0 - - + -
62H VAL* 3.6 35.2 - - + -
104H PHE* 4.8 9.6 - - + -
105H TYR* 1.3 79.6 - - - +
107H PRO* 1.4 78.9 - - + +
110H VAL* 4.7 1.8 - - + -
116H SER* 3.4 3.3 - - - -
117H PHE* 3.0 52.6 + - + +
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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
------------------------------------------------------------
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