Contacts of the strand formed by residues 93 - 109 (chain H) in PDB entry 4FAO
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 PRO 93 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE* 4.1 18.2 - - + -
85H LEU* 4.1 12.3 - - + -
86H TYR 3.6 6.5 - - - +
87H LYS* 4.8 0.9 - - + -
91H GLY 3.6 4.7 - - - +
92H VAL* 1.3 88.8 - - + +
94H THR* 1.3 61.1 + - - +
17L ASN* 5.6 0.5 - - - +
46L ARG* 3.5 28.9 - - - +
55L VAL* 4.2 21.2 - - + +
56L LYS* 3.6 16.6 + - - +
81L VAL* 3.9 26.9 - - + -
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Residues in contact with THR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H LEU* 3.0 7.2 - - - +
86H TYR* 2.9 61.6 + - - -
88H ASP* 3.8 21.1 + - - +
92H VAL* 2.9 20.5 + - + +
93H PRO* 1.3 74.0 - - - +
95H LEU* 1.3 62.0 + - - +
21L GLU* 3.3 28.0 - - + +
56L LYS* 4.1 6.5 - - - +
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Residues in contact with LEU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H SER* 4.5 0.7 - - - -
84H VAL 3.1 26.2 - - - +
85H LEU* 4.3 7.6 - - + +
86H TYR* 4.3 3.1 - - - -
94H THR* 1.3 79.9 - - - +
96H LYS* 1.3 76.2 + - - +
97H TYR* 3.6 22.0 + - + +
13L TYR* 6.3 2.7 - - + -
21L GLU* 5.4 0.6 + - - -
42L TYR* 3.0 39.9 - - + +
56L LYS* 4.2 12.1 - - - +
59L CYS 4.6 4.0 - - - +
60L TRP* 4.1 15.7 - - + -
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Residues in contact with LYS 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ILE 4.0 2.1 - - - +
83H SER* 3.4 1.0 - - - -
84H VAL* 2.9 39.9 + - + +
86H TYR* 3.8 17.0 - - + -
95H LEU* 1.3 77.7 + - - +
97H TYR* 1.3 78.3 + - - +
98H HIS* 3.4 44.1 - - - +
99H TYR* 4.0 19.4 + - + +
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Residues in contact with TYR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ILE 3.4 8.0 - - - +
83H SER* 2.7 40.8 + - - -
95H LEU* 3.6 17.8 + - + +
96H LYS* 1.3 87.0 - - - +
98H HIS* 1.3 86.2 + + - +
29L GLU* 5.3 10.3 - - - -
31L CYS* 3.9 5.1 - - - +
32L GLU* 3.0 37.4 + - + -
39L LEU* 4.5 0.9 - - - +
59L CYS* 3.3 50.3 - - + +
60L TRP* 3.6 5.7 + - - -
61L LEU* 3.6 22.3 - - + +
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Residues in contact with HIS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H PRO* 4.0 19.0 - - + +
96H LYS* 3.4 23.5 - - - +
97H TYR* 1.3 109.4 - + + +
99H TYR* 1.3 58.6 + - - +
100H GLU* 3.1 35.6 + - + +
32L GLU* 4.2 19.8 + - + +
33L GLY* 5.6 1.7 - - - -
61L LEU* 4.6 7.3 - - + +
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Residues in contact with TYR 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LYS* 3.8 22.2 - - + +
17H PHE* 6.2 1.1 - + - -
22H TRP* 4.6 8.9 - + - -
25H TRP* 4.0 18.7 - + - -
26H ILE* 5.5 1.8 - - + -
81H PRO* 3.1 17.0 - - - +
82H ILE* 3.0 25.1 + - + +
84H VAL* 3.9 32.5 - - + -
96H LYS* 4.0 22.8 - - + +
97H TYR 3.6 0.4 - - - -
98H HIS* 1.3 69.9 - - - +
100H GLU* 1.3 68.4 + - - +
102H MET* 3.7 30.3 - - + +
75I GLU* 2.5 37.2 + - - +
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Residues in contact with GLU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LYS* 3.8 20.4 - - - +
79H LEU 4.2 5.9 - - - +
81H PRO* 3.4 22.1 - - - +
98H HIS* 3.1 37.7 + - + +
99H TYR* 1.3 81.1 - - - +
101H GLY* 1.3 68.2 + - - +
102H MET* 3.7 1.2 + - - +
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Residues in contact with GLY 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G THR* 5.9 0.4 - - - -
53G LYS* 3.0 8.9 + - - +
54G HIS* 2.9 28.1 + - - +
79H LEU* 3.8 33.2 + - - +
80H SER 3.8 5.6 + - - -
99H TYR 3.7 0.8 + - - -
100H GLU* 1.3 80.8 + - - +
102H MET* 1.3 59.4 + - - +
103H SER 3.7 1.1 - - - -
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Residues in contact with MET 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LYS* 3.8 23.8 - - - -
54G HIS* 3.7 10.9 - - - +
57G VAL* 4.2 17.0 - - + -
17H PHE* 4.3 13.2 - - + -
22H TRP* 4.7 3.4 - - + -
32H TYR* 2.8 56.4 + - + +
34H ALA* 3.4 6.9 - - - +
80H SER 3.1 3.6 + - - -
82H ILE* 3.8 32.1 - - + -
99H TYR* 3.7 40.6 - - + +
100H GLU 3.8 4.5 - - - +
101H GLY* 1.3 78.7 - - - +
103H SER* 1.3 60.2 + - - +
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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
----------------------------------------------------------
54G HIS* 4.3 1.1 - - - -
33H GLU 3.1 22.7 + - - -
34H ALA* 4.2 4.9 - - - +
35H TYR* 3.6 14.4 - - - -
79H LEU* 3.1 11.0 - - - +
80H SER* 3.0 42.3 + - - -
82H ILE* 4.2 15.9 - - - -
101H GLY 3.7 0.2 - - - -
102H MET* 1.3 80.9 - - - +
104H VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G HIS* 3.3 33.0 - - + +
10H LYS* 4.0 16.0 + - + -
35H TYR* 3.1 48.5 - - + +
36H GLU* 4.4 1.1 - - - +
37H CYS* 3.9 17.9 - - - -
76H PRO* 4.0 17.0 - - + -
79H LEU* 3.7 3.6 - - + -
80H SER* 4.8 1.8 - - - -
103H SER* 1.3 77.1 + - - +
105H ALA* 1.3 63.8 + - - +
106H GLU 3.7 22.9 - - - +
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Residues in contact with ALA 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LYS* 3.2 24.1 + - - +
78H LYS* 2.8 46.6 + - + +
79H LEU 4.0 1.6 - - - +
80H SER* 4.1 20.0 - - - +
103H SER 3.5 1.0 + - - -
104H VAL* 1.3 74.8 - - - +
106H GLU* 1.3 66.5 - - + +
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Residues in contact with GLU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LYS* 5.1 0.7 - - - +
76H PRO* 3.6 5.2 - - - +
77H THR* 2.8 34.9 + - - +
78H LYS* 3.4 38.0 + - + +
104H VAL* 3.7 6.9 - - - +
105H ALA* 1.3 85.3 - - + +
107H CYS* 1.3 62.2 + - - +
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Residues in contact with CYS 107 (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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8H CYS* 4.7 1.8 - - - -
9H GLN* 3.7 13.5 - - - -
10H LYS* 3.7 32.3 - - + +
37H CYS* 2.0 52.5 - - + -
48H ASP 4.4 9.3 - - - +
49H VAL* 5.7 1.1 - - + -
50H THR* 4.3 8.5 + - - -
74H CYS* 4.6 5.8 - - - -
75H VAL 3.5 4.0 - - - -
77H THR* 3.3 11.7 + - - +
104H VAL* 4.1 1.1 - - - -
106H GLU* 1.3 75.5 - - - +
108H GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 108 (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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8H CYS* 4.5 4.1 - - - -
49H VAL* 3.5 19.3 - - - -
50H THR* 5.0 0.2 - - - -
73H CYS 3.3 0.3 - - - +
74H CYS* 3.3 6.6 - - - -
75H VAL* 2.9 34.8 + - - +
77H THR* 3.4 13.7 - - - -
107H CYS* 1.3 78.8 - - - +
109H CYS* 1.3 62.1 + - - -
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Residues in contact with CYS 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H CYS* 4.4 7.9 - - - -
41H CYS* 2.0 56.3 - - + -
45H LEU* 4.7 14.4 - - + -
49H VAL* 3.1 34.2 + - + +
51H PRO* 4.0 4.2 - - + +
55H ALA* 3.8 11.1 - - + +
72H ALA* 4.3 4.9 - - + -
73H CYS 3.4 2.5 - - - -
108H GLY* 1.3 73.5 - - - -
110H ARG* 1.3 85.6 + - - +
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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
------------------------------------------------------------
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