Contacts of the strand formed by residues 99 - 115 (chain B) in PDB entry 1FZV
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 SER 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.8 6.1 - - - +
91B LYS* 2.6 59.2 + - - +
97B ARG* 3.8 9.4 - - - -
98B PRO* 1.3 77.1 + - - +
100B TYR* 1.3 64.9 + - - +
101B VAL* 4.9 1.5 - - - +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.5 42.2 - + + -
88B GLN* 3.7 33.7 - - + +
89B LEU 3.1 17.7 - - - +
90B LEU* 3.8 25.5 - - + +
99B SER* 1.3 79.5 + - - +
101B VAL* 1.3 66.3 + - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 4.6 7.6 - - + -
87B MET 3.5 1.0 - - - +
88B GLN* 3.3 4.1 - - - -
89B LEU* 2.6 49.4 + - + +
91B LYS* 3.6 43.3 - - + +
99B SER* 4.4 2.9 - - - +
100B TYR* 1.3 79.3 - - - +
102B GLU* 1.3 65.9 + - - +
103B LEU* 3.8 21.0 + - + -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.5 39.3 - - + +
86B THR* 4.1 13.0 - - + +
87B MET 3.4 3.6 - - - -
88B GLN* 4.9 8.1 + - + +
101B VAL* 1.3 78.9 - - - +
103B LEU* 1.3 65.5 + - - +
104B THR 4.3 0.7 + - - -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.9 12.3 - - + -
48B TYR* 3.3 24.9 - - + +
56B PHE* 3.8 26.7 - - + -
86B THR* 4.1 0.9 - - - -
87B MET 2.6 42.3 + - - +
89B LEU* 4.3 8.5 - - + -
101B VAL* 3.8 18.1 + - + +
102B GLU* 1.3 79.9 - - - +
104B THR* 1.3 60.4 + - - +
105B PHE* 3.6 36.2 - - + -
202B MPD 4.3 16.6 - - + -
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN* 3.3 37.9 - - + +
85B VAL 3.3 6.1 - - - +
86B THR* 2.7 24.2 + - - +
102B GLU 4.2 0.6 + - - -
103B LEU* 1.3 71.8 - - - +
105B PHE* 1.3 59.4 + - - +
202B MPD 2.5 40.8 + - - +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 4.0 19.5 - - + -
47B GLU* 4.2 14.4 - - + +
61B VAL* 4.0 20.2 - - + -
63B LEU* 3.5 35.4 - - + -
84B ASN* 3.4 7.9 - - - +
85B VAL* 2.8 36.0 + - + +
87B MET* 4.0 30.5 - - + -
89B LEU* 4.4 1.8 - - + -
103B LEU* 3.6 46.2 - - + -
104B THR* 1.3 77.1 - - - +
106B SER* 1.3 61.8 + - - +
202B MPD 3.6 24.7 - - + -
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU* 5.0 3.2 + - - -
63B LEU* 3.8 5.2 - - - +
65B ARG* 2.8 39.3 + - - +
82B THR* 4.8 5.9 - - - +
83B ALA 3.7 6.6 + - - -
84B ASN* 5.0 2.2 - - - -
105B PHE* 1.3 73.6 - - - +
107B GLN* 1.3 63.1 + - - +
108B HIS* 3.9 19.2 + - - -
202B MPD 5.3 1.0 + - - -
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B SER 4.9 2.8 + - - -
63B LEU* 3.4 16.4 - - - +
64B LEU* 2.7 50.6 + - + +
82B THR* 3.1 9.0 - - - -
83B ALA* 2.7 52.4 + - + +
84B ASN* 4.0 9.9 - - - +
85B VAL* 3.8 27.1 - - + +
87B MET* 5.4 0.2 - - - +
105B PHE 4.7 0.2 - - - +
106B SER* 1.3 74.1 - - - +
108B HIS* 1.3 65.9 + - - +
109B VAL* 5.1 2.7 - - + -
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Residues in contact with HIS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 3.4 10.5 - - - +
64B LEU* 3.1 40.3 + - - +
65B ARG* 3.6 27.8 + - - -
66B CYS* 3.0 45.4 + - + +
79B PRO* 4.1 21.4 - - + +
81B GLU 3.9 3.8 - - - -
82B THR* 4.1 12.6 - - + +
106B SER* 3.9 12.5 + - - -
107B GLN* 1.3 78.8 - - - +
109B VAL* 1.3 59.3 + - - +
110B ARG 3.8 0.4 - - - -
111B CYS* 4.6 0.4 - - - -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 3.7 12.0 - - - +
64B LEU* 5.1 5.8 - - + +
81B GLU* 2.9 34.0 + - + +
82B THR 3.9 9.9 - - - +
83B ALA* 3.5 32.5 - - + +
107B GLN* 4.4 4.9 - - + +
108B HIS* 1.3 74.6 - - - +
110B ARG* 1.3 68.8 + - + +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 4.8 0.9 - - - -
79B PRO* 3.4 6.4 - - - +
80B VAL* 2.9 53.7 + - + +
81B GLU* 2.7 41.8 + - + +
109B VAL* 1.3 91.8 - - + +
111B CYS* 1.3 66.1 + - - +
112B GLU* 5.0 5.9 + - - +
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Residues in contact with CYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B CYS* 3.6 21.8 - - - +
36B ARG* 4.0 8.7 - - - +
37B ALA* 3.4 24.8 - - - +
66B CYS* 2.0 55.2 - - + -
77B CYS* 3.9 0.9 - - - -
78B VAL 3.2 5.4 - - - +
79B PRO* 4.1 0.2 - - - -
80B VAL* 4.2 1.9 - - - +
108B HIS* 4.6 1.1 - - - -
110B ARG* 1.3 78.8 - - - +
112B GLU* 1.3 72.8 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 6.2 1.1 - - - -
35B CYS* 3.5 9.6 - - - -
78B VAL* 2.7 44.0 + - - +
80B VAL* 3.6 23.8 - - + +
110B ARG* 5.0 5.0 + - - -
111B CYS* 1.3 83.1 - - - +
113B CYS* 1.3 58.3 + - - +
114B ARG* 2.4 42.1 + - - +
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Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 3.3 30.4 + - - +
35B CYS* 3.4 19.0 - - - +
70B CYS* 2.0 51.4 - - + +
75B LEU* 4.5 12.7 - - + +
76B HIS 3.4 5.4 - - - -
112B GLU* 1.3 74.7 - - - +
114B ARG* 1.3 74.9 + - - +
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.3 7.8 - - - +
76B HIS* 2.8 40.3 + - + +
78B VAL* 3.6 27.1 - - + +
80B VAL* 3.8 15.6 - - - +
112B GLU* 2.4 37.7 + - - +
113B CYS* 1.3 88.9 + - - +
115B PRO* 1.3 77.7 - - + +
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Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASN 3.8 1.3 - - - +
75B LEU* 3.7 19.5 - - + -
76B HIS* 3.3 9.4 + - - -
114B ARG* 1.3 96.6 - - + +
116B LEU* 1.3 68.9 + - - +
117B ARG 3.3 7.5 + - - -
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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